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Search: Posts Made By: carolW
Forum: Bioinformatics 03-25-2016, 12:24 AM
Replies: 2
Views: 1,617
Posted By carolW
can the clinical significance values be used as...

can the clinical significance values be used as they are extracted or any other info from the same or other sources such as statistical significance be associated?
Forum: Bioinformatics 03-24-2016, 08:16 AM
Replies: 2
Views: 1,617
Posted By carolW
extract clinical significant of a vcf variants from clinvar

how can I extract the clinical significant of variants of my vcf file from clinvar? Should I parse the clinvar xml file and match the variants of vcf with those in clinvar if they are annotated...
Forum: Ion Torrent 03-08-2016, 10:19 AM
Replies: 2
Views: 1,796
Posted By carolW
True that could get around the problem. ...

True that could get around the problem.

Cheers,
Forum: Ion Torrent 03-08-2016, 09:11 AM
Replies: 2
Views: 1,796
Posted By carolW
sam input of tmap

one of the input format that tmap accepts is sam. I have generated sam file from basecaller bam with samtools view -h which contains lines starting with @PG and @RG and the raw reads. When I map...
Forum: Ion Torrent 03-04-2016, 04:29 AM
Replies: 0
Views: 1,993
Posted By carolW
BaseCaller program

it might be trivial but how the barcode file should be created for BaseCaller program invoked on command line?

I have created a file as follows

seq1,ACGT,
seq2,TGCA,ATA

but I get an err...
Forum: Bioinformatics 02-10-2016, 03:59 AM
Replies: 15
Views: 3,172
Posted By carolW
yes, if the bam-start will be the sam as bam_new?...

yes, if the bam-start will be the sam as bam_new? does the file size not matter?
Forum: Bioinformatics 02-10-2016, 03:37 AM
Replies: 15
Views: 3,172
Posted By carolW
If picard converts bam2fastq and fastq2bam, is...

If picard converts bam2fastq and fastq2bam, is there any way to have the original bam through these 2 conversions? If so, which parameters to use and if not, why? what would differ between 2 bams?
Forum: Bioinformatics 01-29-2016, 05:23 AM
Replies: 15
Views: 3,172
Posted By carolW
and how are pigz, Pbzip compared with cram of...

and how are pigz, Pbzip compared with cram of EBI? Does Pbzip compress even at a higher level than CRAM?

The original data are BAM. bam can very well be used for alignment but I convert to fastq...
Forum: Bioinformatics 01-28-2016, 08:47 AM
Replies: 15
Views: 3,172
Posted By carolW
as a matter of fact, I want to convert bam2fastq...

as a matter of fact, I want to convert bam2fastq as fastq takes less space and yes the bams are unaligned. in parallel, i wanted to have a tool that converts the reverse to find out if the fastq...
Forum: Bioinformatics 01-28-2016, 03:58 AM
Replies: 15
Views: 3,172
Posted By carolW
fastq2bam

Hi,
which tools is better to convert fastq2bam? picard or samtools or any other that you may suggest? it seems that picard has different converters depending on from which technology fastq is...
Forum: Ion Torrent 01-25-2016, 01:27 AM
Replies: 1
Views: 2,193
Posted By carolW
end of run info

Hi,
Is there any way that when a run is finished, the user can find out or be notified that the run is finished? Whether for ex a plugin is used or not, can he receive an email or find out in a file...
Forum: Ion Torrent 01-19-2016, 06:50 AM
Replies: 16
Views: 3,394
Posted By carolW
15G. but I had expected that if there is no...

15G. but I had expected that if there is no enough mem, a msg will be displayed. when I ran without all params like tmap index -f ~/ucscHg19/hg19.fa, no file was created and no msg was displayed....
Forum: Ion Torrent 01-19-2016, 05:43 AM
Replies: 16
Views: 3,394
Posted By carolW
No file was created. In another run, I ran ...

No file was created. In another run, I ran

tmap index -a bwtsw -f ~/ucscHg19/hg19.fa -o 32 -i 1 -H

and got

src/util/tmap_alloc.c:45: in function "tmap_sa_bwt2sa"
sa->sa
fatal error:...
Forum: Ion Torrent 01-19-2016, 01:29 AM
Replies: 16
Views: 3,394
Posted By carolW
I tried to index the hg19 but it seems to stuck....

I tried to index the hg19 but it seems to stuck. What's wrong or which other params should be used?

tmap index -a bwtsw -f ~/ucscHg19/hg19.fa

src/index/tmap_refseq.c:228: in function...
Forum: Ion Torrent 01-18-2016, 06:51 AM
Replies: 16
Views: 3,394
Posted By carolW
it works now. I took all commands from github. ...

it works now. I took all commands from github.

Many thx
Forum: Ion Torrent 01-18-2016, 06:40 AM
Replies: 16
Views: 3,394
Posted By carolW
Where is the build file located (apologies for my...

Where is the build file located (apologies for my ignorance)?

I installed all the suggested packages but got some warnings and errors that I enclose below.

gcc -DHAVE_CONFIG_H -I. -Wall -g...
Forum: Ion Torrent 01-18-2016, 05:56 AM
Replies: 16
Views: 3,394
Posted By carolW
I installed this library but got another error ...

I installed this library but got another error

src/util/../seq/../io/tmap_file.h:8:19: fatal error: bzlib.h: No such file or directory
#include <bzlib.h>

which library should be installed for...
Forum: Ion Torrent 01-18-2016, 05:49 AM
Replies: 16
Views: 3,394
Posted By carolW
tmap aligner

Hi,
I tried to install TMAP but got the following error when invoking make

src/util/../seq/../io/tmap_file.h:6:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>

the ...
Forum: Bioinformatics 09-23-2015, 10:20 AM
Replies: 1
Views: 1,166
Posted By carolW
genome aligner output in sam format

Hi,
might be an easy question but can all genome aligners output the aligned reads in the SAM format? If not, any converter that can convert to sam format?

Thanks

Carol
Forum: Bioinformatics 01-30-2015, 12:21 AM
Replies: 15
Views: 4,318
Posted By carolW
As proteins whose ID starting WP_ are not in this...

As proteins whose ID starting WP_ are not in this file, how to find the info for these proteins?
Forum: Bioinformatics 01-07-2015, 03:33 AM
Replies: 6
Views: 1,146
Posted By carolW
every thing has got clear. thanks for your help

every thing has got clear. thanks for your help
Forum: Bioinformatics 01-06-2015, 01:38 AM
Replies: 6
Views: 1,146
Posted By carolW
OK but if I get different mapped reads for the...

OK but if I get different mapped reads for the same position with differert strand directions, does it mean that the position is on a fragment that coming from both strand directions?
Forum: Bioinformatics 01-06-2015, 01:15 AM
Replies: 6
Views: 1,146
Posted By carolW
In the output of a genomic mapper, I have got...

In the output of a genomic mapper, I have got some positions both on + and - strand. How could they be explained?
Forum: Bioinformatics 01-06-2015, 01:03 AM
Replies: 6
Views: 1,146
Posted By carolW
genomic positions on both directions

Hi,
Can a genomic position be on the forward and reverse strand at the same time? If so, which category of positions has this property? How is it possible to view such positions?

Carol
Forum: Bioinformatics 12-28-2014, 04:20 AM
Replies: 9
Views: 8,025
Posted By carolW
1- I get an err msg when using useData ...

1-
I get an err msg when using useData

mart <- useData("hsapiens_ensembl", mart=mart)
Error: could not find function "useData"

and if it should have been useDataset

mart <-...
Showing results 1 to 25 of 103

 


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