Forum: Bioinformatics
04-11-2014, 12:31 AM
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Replies: 2
Views: 1,334
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Forum: Bioinformatics
03-12-2014, 03:53 AM
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Replies: 1
Views: 5,187
Look in the samtools manual:
BCFTools view...
Look in the samtools manual:
BCFTools view arguments:
-v Output variant sites only (force -c)
So your command becomes:
samtools mpileup -u -l chr1.snps -f hg19.fa sample1_filter_sort.bam |...
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Forum: Bioinformatics
01-13-2014, 07:28 AM
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Replies: 2
Views: 1,334
pacBioToCA fails with single-end data
Hello everyone,
I am trying to correct my pacbio reads with unmated solexa reads. I use the program pacbioToCA for this. After an hour I retrieve the error:
When searching on this error, I...
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Forum: Bioinformatics
09-13-2013, 12:48 AM
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Replies: 1
Views: 3,431
A python script to help?
Written a small python script which will do it for you, you need python 2.7 or higher to execute.
import sys
def writeNewHeader(head, headIn, out):
writeSeq = False
for headLine in...
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Forum: Bioinformatics
09-06-2013, 12:49 AM
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Replies: 4
Views: 4,470
Hi Elias,
You can visualize your SNPs with...
Hi Elias,
You can visualize your SNPs with IGV. CLC Genomics Workbench probably produced vcf files, which you can read into IGV (http://www.broadinstitute.org/software/igv/download) . You have to...
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Forum: Bioinformatics
09-03-2013, 11:12 PM
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Replies: 9
Views: 4,267
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Forum: Bioinformatics
09-02-2013, 06:02 AM
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Replies: 9
Views: 4,267
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Forum: Bioinformatics
09-02-2013, 05:20 AM
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Replies: 9
Views: 4,267
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Forum: Bioinformatics
09-02-2013, 03:25 AM
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Replies: 9
Views: 4,267
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Forum: Bioinformatics
08-21-2013, 11:46 PM
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Replies: 2
Views: 2,244
Thanks!
I have found some additional...
Thanks!
I have found some additional information about this subject at the samtools (http://samtools.sourceforge.net/mpileup.shtml) website:
The BAQ strategy is invoked by default in mpileup. To...
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Forum: Bioinformatics
08-21-2013, 12:37 AM
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Replies: 2
Views: 2,244
how does samtools mpileup handle the md tag
Hello everyone,
How does samtool mpileup handle the md tag?
I want to know this because the samtools calmd program takes over the 8 hours too execute on a single bam file, and my bam files become...
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Forum: Bioinformatics
06-27-2013, 05:34 AM
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Replies: 2
Views: 8,539
Thanks!
This program looks like it does...
Thanks!
This program looks like it does exactly what I want!
[EDIT]
I used this program for combining the vcf files, but the output is not good enough.
We are going to rerun the samtools...
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Forum: Bioinformatics
06-27-2013, 01:52 AM
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Replies: 2
Views: 8,539
multiple vcf files to one multisampled vcf file
Hello everyone,
Does anyone know how I can create one multisampled vcf file of multiple vcf files? Now I have many vcf files which all contain the SNPs of one sample.
Does the program bcftools...
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Forum: Bioinformatics
06-19-2013, 01:21 AM
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Replies: 4
Views: 3,126
Found the answer!
the problem was with bcftools view. Had to use the options -vcg so I retrieved the output as expected!
This command gave me this file:
#CHROM POS ID REF ALT QUAL FILTER INFO ...
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Forum: Bioinformatics
06-19-2013, 12:50 AM
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Replies: 4
Views: 3,126
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Forum: Bioinformatics
06-19-2013, 12:12 AM
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Replies: 4
Views: 3,126
I think I have found the problem...
Samtools...
I think I have found the problem...
Samtools mpileup doesn't create a vcf file by default but a file in pileup format.
Now I am using the -ug option and piping the output to bcftools view.
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Forum: Bioinformatics
06-18-2013, 11:59 PM
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Replies: 4
Views: 3,126
Samtools mpileup finds SNPs on each position
Hello everyone,
I am trying to use samtools mpileup. I am using the settings:
samtools mpileup -f ../chr12Ref.fa chr12.bam > chr12.vcf
When I look in the output, I see this result:
SL2_40ch12...
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Forum: Bioinformatics
05-28-2013, 01:08 AM
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Replies: 5
Views: 3,546
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Forum: Bioinformatics
05-16-2013, 07:10 AM
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Replies: 0
Views: 1,218
Tophat only maps a few reads
Hello everyone,
I use the data from the sra (http://sra.dnanexus.com/runs/SRR493747/samples) website.
for executing Tophat I use the command:
tophat2 -a 5 -m 2 -N 10 -x 1 --read-edit-dist 12 -o...
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Forum: RNA Sequencing
03-26-2013, 06:32 AM
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Replies: 5
Views: 4,067
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Forum: Bioinformatics
03-18-2013, 02:53 AM
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Replies: 0
Views: 1,389
Tophat colorspace problem --integer-quals 0
Hello everyone,
Is there an tophat option for setting the --integer-quals to 0 when using colorspace reads? I have a fastq file with phred33 quality. According to the manual when using the --color...
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Forum: Bioinformatics
02-18-2013, 12:54 AM
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Replies: 5
Views: 6,123
Does the command ls -l...
Does the command ls -l /st_Users/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome*.ebwt return all 6 ebwt files you downloaded?
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Forum: Bioinformatics
02-12-2013, 04:59 AM
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Replies: 1
Views: 1,390
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Forum: Bioinformatics
02-12-2013, 04:52 AM
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Replies: 1
Views: 1,390
Tophat gtf problem
Hello everyone,
I am using tophat with a gtf file. I used it once with this command:
/home/sge_share_fedor8/common_scripts/tophat-2.0.6/tophat2 --color --quals --GTF...
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Forum: Bioinformatics
02-04-2013, 01:50 AM
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Replies: 6
Views: 1,760
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