SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 38
Search took 0.00 seconds.
Search: Posts Made By: Jetse
Forum: Bioinformatics 04-11-2014, 12:31 AM
Replies: 2
Views: 1,334
Posted By Jetse
I did not solve this problem...

I did not solve this problem...
Forum: Bioinformatics 03-12-2014, 03:53 AM
Replies: 1
Views: 5,187
Posted By Jetse
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 |...
Forum: Bioinformatics 01-13-2014, 07:28 AM
Replies: 2
Views: 1,334
Posted By Jetse
Unhappy 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...
Forum: Bioinformatics 09-13-2013, 12:48 AM
Replies: 1
Views: 3,431
Posted By Jetse
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...
Forum: Bioinformatics 09-06-2013, 12:49 AM
Replies: 4
Views: 4,470
Posted By Jetse
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...
Forum: Bioinformatics 09-03-2013, 11:12 PM
Replies: 9
Views: 4,267
Posted By Jetse
How did you solve it? So other people who find...

How did you solve it?
So other people who find this thread with the same problem can try your solution too...
Forum: Bioinformatics 09-02-2013, 06:02 AM
Replies: 9
Views: 4,267
Posted By Jetse
It could be your computer ran out of memory, then...

It could be your computer ran out of memory, then sorting would solve your problem.

From the manual:
Forum: Bioinformatics 09-02-2013, 05:20 AM
Replies: 9
Views: 4,267
Posted By Jetse
What is your output when you use the command: ...

What is your output when you use the command:
bedtools intersect -a A.bed -b B.bed -wao | less
Do you see a lot of output, all with a zero at the end? (this means they don't have overlaps)
Forum: Bioinformatics 09-02-2013, 03:25 AM
Replies: 9
Views: 4,267
Posted By Jetse
What is the command you used? How do the files...

What is the command you used?
How do the files look like?
Forum: Bioinformatics 08-21-2013, 11:46 PM
Replies: 2
Views: 2,244
Posted By Jetse
Thumbs up 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...
Forum: Bioinformatics 08-21-2013, 12:37 AM
Replies: 2
Views: 2,244
Posted By Jetse
Post 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...
Forum: Bioinformatics 06-27-2013, 05:34 AM
Replies: 2
Views: 8,539
Posted By Jetse
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...
Forum: Bioinformatics 06-27-2013, 01:52 AM
Replies: 2
Views: 8,539
Posted By Jetse
Question 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...
Forum: Bioinformatics 06-19-2013, 01:21 AM
Replies: 4
Views: 3,126
Posted By Jetse
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 ...
Forum: Bioinformatics 06-19-2013, 12:50 AM
Replies: 4
Views: 3,126
Posted By Jetse
That was indeed my problem, but now I converted...

That was indeed my problem, but now I converted this to vcf format by using the -ug option and piping this output to bcftools view. Now my output looks like this:
#CHROM POS ID REF ALT...
Forum: Bioinformatics 06-19-2013, 12:12 AM
Replies: 4
Views: 3,126
Posted By Jetse
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.
Forum: Bioinformatics 06-18-2013, 11:59 PM
Replies: 4
Views: 3,126
Posted By Jetse
Unhappy 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...
Forum: Bioinformatics 05-28-2013, 01:08 AM
Replies: 5
Views: 3,546
Posted By Jetse
I also had a memory leak, I could solve this by...

I also had a memory leak, I could solve this by sorting my bam files.

(this was highest hit when googeling memory leak of mpileup and this is a common mistake)
Forum: Bioinformatics 05-16-2013, 07:10 AM
Replies: 0
Views: 1,218
Posted By Jetse
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...
Forum: RNA Sequencing 03-26-2013, 06:32 AM
Replies: 5
Views: 4,067
Posted By Jetse
Did anyone of you solve this problem? I have...

Did anyone of you solve this problem?
I have exactly the same problem now.

Mapping left_kept_reads to genome GRCh37_gatk_colorspace with Bowtie
Mapping left_kept_reads_seg1 to genome...
Forum: Bioinformatics 03-18-2013, 02:53 AM
Replies: 0
Views: 1,389
Posted By Jetse
Angry 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...
Forum: Bioinformatics 02-18-2013, 12:54 AM
Replies: 5
Views: 6,123
Posted By Jetse
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?
Forum: Bioinformatics 02-12-2013, 04:59 AM
Replies: 1
Views: 1,390
Posted By Jetse
Had to read the manual better... I hope this...

Had to read the manual better...

I hope this will fix it ;)
Forum: Bioinformatics 02-12-2013, 04:52 AM
Replies: 1
Views: 1,390
Posted By Jetse
Question 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...
Forum: Bioinformatics 02-04-2013, 01:50 AM
Replies: 6
Views: 1,760
Posted By Jetse
The fasta file from which the bowtie index is...

The fasta file from which the bowtie index is made. When you have downloaded the bowtie index, and not created the bowtie index from a fasta file, you always get this warning.
Showing results 1 to 25 of 38

 


All times are GMT -8. The time now is 07:44 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO