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Software tools for detecting Copy Number Variations (CNV) smice Bioinformatics 24 11-10-2014 02:59 AM
CNV Simulator -- Random Number Generation gprakhar Bioinformatics 5 05-11-2012 10:34 PM
tools to detect copy number variants nans_bn Bioinformatics 2 01-12-2012 05:25 AM
PubMed: Detecting copy number variation with mated short reads. Newsbot! Literature Watch 0 02-18-2011 12:00 PM
CNV variation effects on exome sequencing? wrighth Bioinformatics 0 12-21-2010 12:43 PM

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Old 11-24-2011, 03:58 AM   #21
DineshCyanam
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Quote:
Originally Posted by parveendabas View Post
Thank you dinesh. But my data is not normal/control type and neither its related to 1000 genome project. Its one sample data. What should i do??
Well you still need to compare it with against a normal. See post #9 above.
http://seqanswers.com/forums/showthread.php?p=40537

or

try CNVnator from Mark Gerstein's lab. You don't need to supply a ref file for CNVnator. More info and link to papers here: http://sv.gersteinlab.org/
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Old 01-30-2012, 10:13 PM   #22
difereg
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Hello!
Does the CNV-seq be used in genome (sequenced by Illumina -Short reads) in haploids apicomplexa?
Any thoughs?
Thanks a lot.
difereg
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Old 02-19-2012, 03:40 AM   #23
findingdan
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Quote:
Originally Posted by mimi_lupton View Post
Dear all,
I have a couple of questions regarding CNV-seq.
I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work fine, but some file combinations come up with an error, which is strange as all the data has been produced and analysed in exactly the same way. The error is;

"Can't use an undefined value as an ARRAY reference at /share/apps/cnv-seq_1.0/bin/cnv-seq.pl line 204, <REF> line 6460211."

I think this is some kind of Perl script error??

Also does anyone have any experience of using capture data with CNV-seq? any advice would be greatly appreciated.

Thanks for you help
Ever get an answer for this 'value as an ARRAY reference" problem? i'm having the same issue..
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Old 04-04-2012, 01:33 AM   #24
adurasiwam3
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Default help

I'm running the CNV-seq package and I keep getting the following error:

write read-counts into file: test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.count
R package cnv output: test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv
Error in library(cnv) : there is no package called 'cnv'
Execution halted

Can someone please help me out?

Btw, the data I'm using is the sample data available on the CNV-seq website.

Thank you
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Old 04-05-2012, 06:09 AM   #25
pd
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Default Can't use an undefined value as an ARRAY reference

While running CNV-seq, sometimes it works perfectly but sometimes i end with the following error "Can't use an undefined value as an ARRAY reference at line 205, <REF> line 1119928258".
The same has been asked many a times but no solution yet. Anyone to help out or some other suggestion for alternate CNV detection algorithms?
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Old 04-19-2012, 04:07 PM   #26
ragowthaman
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@adurasiwam3:
It indicates, you dont have the CNV R package installed into correct place (or at all).

Assuming your machine has R.
you install the package by issuing following command while inside the package's root folder.

R CMD INSTALL /cnv/

If your syestem's R is not in the path, you need to call it explicitly (eg. /apps/bin/R) instead of R.

Hope this helps.
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Old 05-11-2012, 10:43 PM   #27
adurasiwam3
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it helped!

thank you ragowthaman
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Old 05-11-2012, 10:44 PM   #28
adurasiwam3
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can someone explain how the sensitivity/specificity for CNV-seq is calculated in the CNV-seq paper?

Where can I get data with simulated CNVs (including the known positions)?

Thank you!
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Old 09-28-2012, 08:28 PM   #29
billthebrute
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Hi CNV-seq users. I am having a bit of trouble understanding how the cnv caller works.

The results of one of my .cnv files is as follows:


"22" 16275937 18988591 204 2822 17632264 -0.683143010100174 2.46090424342812e-08 0 NA NA NA
"22" 17632265 20344919 195 3190 18988592 -0.925076474377026 2.85143491959854e-12 0 NA NA NA
"22" 18988593 21701247 191 3107 20344920 -0.916943777560497 3.8950753868117e-12 0 NA NA NA
"22" 20344921 23057575 188 3082 21701248 -0.928128374311553 2.53633054795169e-12 0 NA NA NA
"22" 21701249 24413903 210 3108 23057576 -0.780591350215992 6.85565176334874e-10 0 NA NA NA
"22" 23057577 25770231 206 3256 24413904 -0.875450536557434 1.90371570869566e-11 0 NA NA NA
"22" 24413905 27126559 177 3139 25770232 -1.04154984297352 3.22421238629005e-14 0 NA NA NA
"22" 25770233 28482887 180 3103 27126560 -1.00066096467345 1.55775796481263e-13 0 NA NA NA
"22" 27126561 29839215 157 2718 28482888 -1.00677507135017 1.23086398489238e-13 0 NA NA NA
"22" 28482889 31195543 143 2606 29839216 -1.08081611126415 7.11362307806884e-15 0 NA NA NA
"22" 29839217 32551871 160 2852 31195544 -1.04889625103093 2.42971963892229e-14 0 NA NA NA
"22" 31195545 33908199 155 2827 32551872 -1.08199784203134 6.7976211176428e-15 0 NA NA NA
"22" 32551873 35264527 166 2610 33908200 -0.867860739584727 2.5422391389699e-11 0 NA NA NA
"22" 33908201 36620855 170 2621 35264528 -0.839576781665121 7.44538364328285e-11 0 NA NA NA
"22" 35264529 37977183 210 3210 36620856 -0.827178143817948 1.19029886619997e-10 0 NA NA NA
"22" 36620857 39333511 218 3208 37977184 -0.772340181152399 9.32704407763649e-10 0 NA NA NA
"22" 37977185 40689839 195 2891 39333512 -0.783088659201844 6.24484354174541e-10 0 NA NA NA
"22" 39333513 42046167 191 2608 40689840 -0.664365405669734 4.82741849789952e-08 0 NA NA NA
"22" 40689841 43402495 306 4365 42046168 -0.727444175298556 4.90998416767461e-09 0 NA NA NA
"22" 42046169 44758823 409 5386 43402496 -0.612107561034328 3.04270126227705e-07 0 NA NA NA
"22" 43402497 46115151 273 3718 44758824 -0.660619993474034 5.51777958936528e-08 0 NA NA NA
"22" 44758825 47471479 193 3190 46115152 -0.939949750858556 1.61095440200424e-12 0 NA NA NA

Surely this should have been annotated as a cnv as there are more than 4 windows with a log2<-0.6 and high significance !
Moreover I find the coordinates strange:
look at the first and third line:
"22" 16275937 18988591
"22" 18988593 21701247

18988591 is not equal to 18988593. Whereas sometimes, if I change the window size the end of the first line and the beginning of the third would be the same.

These files were created with default values, window size = 2712655

Thanks in advance for any insight you can give me. I am tempted to call the cnvs manually...what would be the best way to do so from the .cnv file ?
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Old 11-13-2012, 03:56 AM   #30
jterol
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Hi!
I've got a chromosome with 3 deletions and woudl like to have them all in the same plot, but it seems I can only choose 1 CNV at a time:
>plot.cnv(data, CNV=2, upstream=2e+6, downstream=2e+6)

Any suggesion?
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Old 11-13-2012, 07:29 AM   #31
jordiet
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Quote:
Originally Posted by jterol View Post
Hi!
I've got a chromosome with 3 deletions and woudl like to have them all in the same plot, but it seems I can only choose 1 CNV at a time:
>plot.cnv(data, CNV=2, upstream=2e+6, downstream=2e+6)

Any suggesion?
Hi

in the R package for the cnv-seq (cnv-seq manual) there is a function to do it:

plot.cnv.chr <- function (data, chromosome = NA, from = NA, to = NA, title = NA, ylim = c(-4, 4), glim = c(NA, NA), xlabel = "Position (bp)")

Unfortunately I've tried to use it several times and I couldn't get it...

Let me know if you get it!
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Old 11-13-2012, 11:33 PM   #32
jterol
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Well,

after some struggling I executed:
>plot.cnv(data, ylim = c(-2,2))
And got all the deletions and the whole chromosome, and even managed to limit the log2(ratio) to the ones I wanted. So the trock was not to choose any CNV!
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Old 03-15-2013, 10:03 AM   #33
Ayush_Saxena
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Default Bugs

Is there any way we can report a bug for CNV-Seq, I tried searching for it but couldn't find.

the software, for some strange reasons is not calling CNVs even when all conditions are met. I used a log2 threshold of 0.8 and a window size of only 2 so that I can look at the result(cnv.print()) by eye and judge which ones to pick.

"CHROMOSOME_II" 1450045 1451171 404 416 1450608 0.881401332001257 2.29121717076986e-13 0 NA NA NA
"CHROMOSOME_II" 1450609 1451735 570 464 1451172 1.22046668131509 1.31845290945157e-22 0 NA NA NA
"CHROMOSOME_II" 1451173 1452299 629 550 1451736 1.11725796585782 1.18360892978282e-19 0 NA NA NA
"CHROMOSOME_II" 1451737 1452863 671 657 1452300 0.954048963268409 3.24101505961822e-15 0 NA NA NA
"CHROMOSOME_II" 1452301 1453427 602 577 1452864 0.984821735504775 5.02877099034994e-16 0 NA NA NA
"CHROMOSOME_II" 1452865 1453991 513 516 1453428 0.915217327574355 3.2389370038797e-14 0 NA NA NA
"CHROMOSOME_II" 1453429 1454555 590 516 1453992 1.1169734562165 1.20564598087743e-19 0 NA NA NA
"CHROMOSOME_II" 1453993 1455119 551 465 1454556 1.16845116996632 4.16186035989176e-21 0 NA NA NA
"CHROMOSOME_II" 1454557 1455683 374 369 1455120 0.943047021217795 6.25787394726544e-15 0 NA NA NA
"CHROMOSOME_II" 1455121 1456247 415 422 1455684 0.899497904917657 8.08876111589643e-14 0 NA NA NA
"CHROMOSOME_II" 1455685 1456811 615 573 1456248 1.02568083886025 4.03369375071261e-17 0 NA NA NA
"CHROMOSOME_II" 1456249 1457375 666 575 1456812 1.13558978863008 3.59196486144447e-20 0 NA NA NA
"CHROMOSOME_II" 1456813 1457939 663 565 1457376 1.15438757020059 1.04963378485956e-20 0 NA NA NA
"CHROMOSOME_II" 1457377 1458503 609 524 1457940 1.14050498375944 2.60576418573692e-20 0 NA NA NA
"CHROMOSOME_II" 1457941 1459067 410 408 1458504 0.930684324924505 1.30371091397085e-14 0 NA NA NA

This entire >8kb region qualifies all conditions set for a CNV to be called and its still not called which makes me a little skeptical about the software itself. Can anyone list some other reliable alternatives
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Old 03-15-2013, 10:09 AM   #34
Ayush_Saxena
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Quote:
Originally Posted by billthebrute View Post
Hi CNV-seq users. I am having a bit of trouble understanding how the cnv caller works.

The results of one of my .cnv files is as follows:


"22" 16275937 18988591 204 2822 17632264 -0.683143010100174 2.46090424342812e-08 0 NA NA NA
"22" 17632265 20344919 195 3190 18988592 -0.925076474377026 2.85143491959854e-12 0 NA NA NA
"22" 18988593 21701247 191 3107 20344920 -0.916943777560497 3.8950753868117e-12 0 NA NA NA
"22" 20344921 23057575 188 3082 21701248 -0.928128374311553 2.53633054795169e-12 0 NA NA NA
"22" 21701249 24413903 210 3108 23057576 -0.780591350215992 6.85565176334874e-10 0 NA NA NA
"22" 23057577 25770231 206 3256 24413904 -0.875450536557434 1.90371570869566e-11 0 NA NA NA
"22" 24413905 27126559 177 3139 25770232 -1.04154984297352 3.22421238629005e-14 0 NA NA NA
"22" 25770233 28482887 180 3103 27126560 -1.00066096467345 1.55775796481263e-13 0 NA NA NA
"22" 27126561 29839215 157 2718 28482888 -1.00677507135017 1.23086398489238e-13 0 NA NA NA
"22" 28482889 31195543 143 2606 29839216 -1.08081611126415 7.11362307806884e-15 0 NA NA NA
"22" 29839217 32551871 160 2852 31195544 -1.04889625103093 2.42971963892229e-14 0 NA NA NA
"22" 31195545 33908199 155 2827 32551872 -1.08199784203134 6.7976211176428e-15 0 NA NA NA
"22" 32551873 35264527 166 2610 33908200 -0.867860739584727 2.5422391389699e-11 0 NA NA NA
"22" 33908201 36620855 170 2621 35264528 -0.839576781665121 7.44538364328285e-11 0 NA NA NA
"22" 35264529 37977183 210 3210 36620856 -0.827178143817948 1.19029886619997e-10 0 NA NA NA
"22" 36620857 39333511 218 3208 37977184 -0.772340181152399 9.32704407763649e-10 0 NA NA NA
"22" 37977185 40689839 195 2891 39333512 -0.783088659201844 6.24484354174541e-10 0 NA NA NA
"22" 39333513 42046167 191 2608 40689840 -0.664365405669734 4.82741849789952e-08 0 NA NA NA
"22" 40689841 43402495 306 4365 42046168 -0.727444175298556 4.90998416767461e-09 0 NA NA NA
"22" 42046169 44758823 409 5386 43402496 -0.612107561034328 3.04270126227705e-07 0 NA NA NA
"22" 43402497 46115151 273 3718 44758824 -0.660619993474034 5.51777958936528e-08 0 NA NA NA
"22" 44758825 47471479 193 3190 46115152 -0.939949750858556 1.61095440200424e-12 0 NA NA NA

Surely this should have been annotated as a cnv as there are more than 4 windows with a log2<-0.6 and high significance !
Moreover I find the coordinates strange:
look at the first and third line:
"22" 16275937 18988591
"22" 18988593 21701247

18988591 is not equal to 18988593. Whereas sometimes, if I change the window size the end of the first line and the beginning of the third would be the same.

These files were created with default values, window size = 2712655

Thanks in advance for any insight you can give me. I am tempted to call the cnvs manually...what would be the best way to do so from the .cnv file ?
I overlooked your post before I posted mine, I'm having a very similar problem and I've also posted my data. Did you get around your problem or called manually?

Last edited by Ayush_Saxena; 03-15-2013 at 10:12 AM. Reason: Forgot to Quote
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Old 03-26-2014, 11:15 AM   #35
clarissaboschi
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Default how to obtain the ref.hits file from a genome reference

Dear members,

I am using data from Illumina next generation sequencing from different chickens. I have different bam files (for each chicken), and I obtained the test.hits using the command line:
samtools view –F 4 file1.bam | perl –lane ‘print “$F[2]\t$F[3]”’ > test1.hits

But I need to have also the ref.hits, but I only have the reference chicken genome reference (fasta file). How can I get this ref.hits?

Thanks
Clarissa
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Old 07-16-2014, 05:02 PM   #36
arcolombo698
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The manual does not specify that mouse genome is not allowed, has anyone used CNV-seq for mouse data?

I was able to add the genome.fa used under alignment under --genome parameter, but wish to confirm If this is correct.

thank you
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Old 07-16-2014, 05:08 PM   #37
arcolombo698
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@ Clarissa

normally with CGH experiments you are comparing a tumor sample with a non-tumor sample. my data has a germline sample and also a tumor sample. the germline is used as a reference. So you should have two samples to compare.

?
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Old 07-16-2014, 06:47 PM   #38
xiechao
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Quote:
Originally Posted by arcolombo698 View Post
The manual does not specify that mouse genome is not allowed, has anyone used CNV-seq for mouse data?

I was able to add the genome.fa used under alignment under --genome parameter, but wish to confirm If this is correct.

thank you
Yes, it should work with any genome. But you need to specify --genome-size, which is used for sliding window size calculation.
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Old 07-16-2014, 07:51 PM   #39
arcolombo698
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Default Rotating the X tick marks with plot.cnv

Thank you... I have a last question

when plotting, how do I rotate 90 degrees the x labels for each tick mark. I know with ggplot there is an angle option that can be used. right now my images look like this


Here is my command

plot.cnv(data)
Warning messages:
1: In plot.cnv.all(data, ...) :
missed some data points due to small ylim range
2: Removed 111874 rows containing missing values (geom_point).
> ggsave("allchroms.pdf")
Saving 6.99 x 6.99 in image
Warning message:
Removed 111874 rows containing missing values (geom_point).



Thank you again very much.

Should I use the reshape package?
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Old 07-16-2014, 07:58 PM   #40
xiechao
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Quote:
Originally Posted by arcolombo698 View Post
Thank you... I have a last question

when plotting, how do I rotate 90 degrees the x labels for each tick mark. I know with ggplot there is an angle option that can be used. right now my images look like this


Here is my command

plot.cnv(data)
Warning messages:
1: In plot.cnv.all(data, ...) :
missed some data points due to small ylim range
2: Removed 111874 rows containing missing values (geom_point).
> ggsave("allchroms.pdf")
Saving 6.99 x 6.99 in image
Warning message:
Removed 111874 rows containing missing values (geom_point).



Thank you again very much.

Should I use the reshape package?
Try something like:
g <- plot.cnv(data, CNV = 4)
g + theme(axis.text.x = element_text(angle = 90))
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