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Forum: Bioinformatics 05-18-2015, 02:41 AM
Replies: 0
Views: 941
Posted By amitbik
SSPACE scaffolding

Hi All,

I am using SSPACE for scaffolding. After running sspace i am getting same no of scaffolds as the no of contigs i got but the no of scaffold should be less then the no of contig. Am i...
Forum: Bioinformatics 09-10-2014, 11:11 PM
Replies: 6
Views: 2,426
Posted By amitbik
Hi Crusoe Thanks a ton..:) It is working...

Hi Crusoe

Thanks a ton..:) It is working fine now.... I will be waiting for next release of khmer.

Cheers,
--
Amit
Forum: Bioinformatics 09-02-2014, 09:34 PM
Replies: 6
Views: 2,426
Posted By amitbik
Error in using normalize-by-median.py

Hi, crusoe

An error is coming while using normalize-by-median.py.

python normalize-by-median.py -h

Traceback (most recent call last):
File "normalize-by-median.py", line 19, in <module>
...
Forum: Bioinformatics 08-05-2014, 09:26 PM
Replies: 0
Views: 959
Posted By amitbik
Error in installation of MAP assembler

Hi All,

I am trying to install MAP assembler for metagenomic assembly but i am getting following error.

make
g++ -O3 -fopenmp -c -o Cons_Ctg_Cons.o Cons_Ctg_Cons.cpp
Cons_Ctg_Cons.cpp: In...
Forum: Literature Watch 07-23-2014, 02:06 AM
Replies: 29
Views: 22,724
Posted By amitbik
Hi, All Please help me...

Hi, All

Please help me guys...:confused::confused:
Forum: Literature Watch 07-22-2014, 03:27 AM
Replies: 29
Views: 22,724
Posted By amitbik
Abyss & ray

Hi, Everyone

I am doing metagenomic shotgun assembly in Abyss and Ray i got the result but i wanted to know how many reads are used and unused?
I tried but failed. can anyone just guide me to...
Forum: Bioinformatics 07-05-2014, 12:26 AM
Replies: 10
Views: 4,636
Posted By amitbik
Thanks a lot bruce01 and Zaag I think there...

Thanks a lot bruce01 and Zaag

I think there is some problem in Rscript thats why it is showing error.
I did as mentioned in the link

http://www.broadinstitute.org/gatk/g...ovariates.html
...
Forum: Bioinformatics 07-04-2014, 02:58 AM
Replies: 10
Views: 4,636
Posted By amitbik
I am trying to plot the graph before and after...

I am trying to plot the graph before and after the baserecalibration.
here is the doc

https://www.broadinstitute.org/gatk//events/2038/GATKwh0-BP-3-Base_recalibration.pdf
Forum: Bioinformatics 07-03-2014, 10:05 PM
Replies: 10
Views: 4,636
Posted By amitbik
Hi All I am getting error in...

Hi All

I am getting error in BaseRecalibrator step. I am using this command

java -Xmx8g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R file.fa -I file_relgn.bam -knownSites snv.sorted.vcf...
Forum: Bioinformatics 04-18-2014, 05:37 AM
Replies: 20
Views: 11,445
Posted By amitbik
Thank you ...maubp Thanks for the...

Thank you ...maubp
Thanks for the information...:)
Forum: Bioinformatics 04-17-2014, 09:21 PM
Replies: 20
Views: 11,445
Posted By amitbik
Hi.... maubp I have one question can it be...

Hi.... maubp

I have one question can it be possible to give the column heading in the tabular format?
After converting from xml to tabular format it confusing to know which column representing...
Forum: Bioinformatics 04-17-2014, 07:03 AM
Replies: 20
Views: 11,445
Posted By amitbik
:)Thank a ton ....:) maubp It worked...

:)Thank a ton ....:) maubp

It worked now.....:)
Forum: Bioinformatics 04-17-2014, 05:29 AM
Replies: 20
Views: 11,445
Posted By amitbik
I am getting this error. $ python...

I am getting this error.

$ python blastxml_to_tabular.py outfmt5.xml outfmt.tsv std
ERROR: The script API has changed, sorry.
Forum: Bioinformatics 04-17-2014, 04:34 AM
Replies: 20
Views: 11,445
Posted By amitbik
Hi..:) maubp I want to convert blast xml...

Hi..:) maubp

I want to convert blast xml output to tabular form. I followed your link but it is not opening.
Can you send the again?

Thank you......
Forum: Bioinformatics 04-10-2014, 05:26 AM
Replies: 14
Views: 7,266
Posted By amitbik
I already did it as they instructed but it is not...

I already did it as they instructed but it is not working. The error is coming like this

$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O3 `glib-config --cflags --libs glib-2.0`"...
Forum: Bioinformatics 04-09-2014, 11:33 PM
Replies: 14
Views: 7,266
Posted By amitbik
Actually i am installing cegma for that i need to...

Actually i am installing cegma for that i need to install geneid,genewise,hmmer and ncbi blast. I have installed all except genewise..:confused:
Forum: Bioinformatics 04-09-2014, 03:06 AM
Replies: 14
Views: 7,266
Posted By amitbik
As you said i did. I am getting error like this ...

As you said i did. I am getting error like this

$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libwisebase.a )
make[1]: Entering directory...
Forum: Bioinformatics 04-09-2014, 12:30 AM
Replies: 14
Views: 7,266
Posted By amitbik
I have installed libgtk3.0 then also i am getting...

I have installed libgtk3.0 then also i am getting error like this


$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libwisebase.a )
make[1]: Entering...
Forum: Bioinformatics 04-08-2014, 10:30 PM
Replies: 14
Views: 7,266
Posted By amitbik
Sorry for late reply.. Thanks for your reply...

Sorry for late reply..
Thanks for your reply GenoMax..:)
I am using ubuntu 14.04 and i have tried the above solutions but still i am getting error..:(

$ make all
(cd base ; make CC="gcc"...
Forum: Bioinformatics 03-29-2014, 01:47 AM
Replies: 14
Views: 7,266
Posted By amitbik
Hi all, I am trying to install genwise and i am...

Hi all,
I am trying to install genwise and i am getting following error

$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libwisebase.a )
make[1]:...
Forum: Bioinformatics 03-02-2014, 09:56 PM
Replies: 2
Views: 985
Posted By amitbik
You can also refer this site. ...

You can also refer this site.

http://picard.sourceforge.net/explain-flags.html
Forum: Bioinformatics 02-12-2014, 08:59 PM
Replies: 17
Views: 3,717
Posted By amitbik
Can any one reply me why i am getting error like...

Can any one reply me why i am getting error like this?? plz reply me guys..:confused:
Forum: Bioinformatics 02-11-2014, 04:08 AM
Replies: 17
Views: 3,717
Posted By amitbik
Thanks for your response :) SES My input...

Thanks for your response :) SES

My input file is 318 mb. I ll tried as you said this time i took 1000 seq. i gave command

ltr_finder -w 0 -s trna.fa -a ./ps_scan/ t.fa > t.txt

No output...
Forum: Bioinformatics 02-10-2014, 08:00 PM
Replies: 17
Views: 3,717
Posted By amitbik
Can any one help me to find out the...

Can any one help me to find out the error.:confused::confused:
Forum: Bioinformatics 02-09-2014, 08:53 PM
Replies: 17
Views: 3,717
Posted By amitbik
Hi :) sunhh, I have some problem in...

Hi :) sunhh,

I have some problem in ltr_finder i am using this command

ltr_finder -w 0 -s trna.fa -a ./ps_scan/ uni.fa > uni_ltr.txt

it run arround 16 hours and the two file uni.fa.ltrf...
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