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Search: Posts Made By: KNS
Forum: Bioinformatics 12-01-2011, 09:55 PM
Replies: 3
Views: 3,292
Posted By KNS
Alishan, two ways to get at counts etc. 1)...

Alishan,
two ways to get at counts etc.
1) Use one of the old samtools versions - 0.1.12a seemed ok.
2) Even better: Use GATK
Forum: Bioinformatics 05-17-2011, 07:39 PM
Replies: 3
Views: 3,292
Posted By KNS
can anyone help?

can anyone help?
Forum: Bioinformatics 05-17-2011, 12:40 AM
Replies: 3
Views: 3,292
Posted By KNS
Question differences in coverage BEDtools - samtools mpileup

Hi,
I have been using samtools mpileup and BEDtools coverageBed under default settings to count coverages at SNP sites identified with samtools mpileup. Both programs used the same paired BAM files...
Forum: Bioinformatics 05-10-2011, 05:45 AM
Replies: 3
Views: 1,357
Posted By KNS
Yes, vcf files can always be viewed from an...

Yes, vcf files can always be viewed from an editor. Check
http://samtools.sourceforge.net/mpileup.shtml
for what the columns mean.
HTH
Forum: Bioinformatics 11-25-2010, 03:11 AM
Replies: 14
Views: 11,542
Posted By KNS
There has been a few issues with the output...

There has been a few issues with the output generated by samtools mpileup - see a couple of recent threads including my post "Unstable output from mpileup/samtools" here in the bioinformatics forum....
Forum: Bioinformatics 11-24-2010, 08:08 PM
Replies: 14
Views: 5,393
Posted By KNS
No further suggestions?

No further suggestions?
Forum: Bioinformatics 11-24-2010, 05:07 AM
Replies: 14
Views: 5,393
Posted By KNS
Running samtools mpileup as suggested on mpileup...

Running samtools mpileup as suggested on mpileup helpfile, however, produces seemingly intact output, which breaks off prematurely. Here, only sequences up to scaffold 8 (of 2518) are processed.
...
Forum: Bioinformatics 11-24-2010, 12:47 AM
Replies: 14
Views: 5,393
Posted By KNS
Unfortunately, the DP4-issue persists with...

Unfortunately, the DP4-issue persists with samtools 0.1.11(and the exact same commands as in the tutorial):
...
Forum: Bioinformatics 11-23-2010, 11:13 PM
Replies: 14
Views: 5,393
Posted By KNS
Thanks for these suggestions, lh3! I will get...

Thanks for these suggestions, lh3!
I will get samtools 0.1.11(2010-11-22). I generated the alignment strictly following the code on the bowtie tutorials:
Index building
bowtie-build...
Forum: Bioinformatics 11-23-2010, 07:08 AM
Replies: 14
Views: 5,393
Posted By KNS
Thanks, didn't know about GATK but now I will...

Thanks, didn't know about GATK but now I will definitely give it a try. I am mostly interested in the actual number of reads per allele (which I could parse out from the sam files manually, but then,...
Forum: Bioinformatics 11-23-2010, 06:49 AM
Replies: 14
Views: 5,393
Posted By KNS
thanks for replying! The mpileup commands were as...

thanks for replying! The mpileup commands were as follows (and this pretty much maches what you suggested, and exactly what is said on the tutorial page):

samtools mpileup -gf ref.fa aln1.bam...
Forum: Bioinformatics 11-23-2010, 01:09 AM
Replies: 2
Views: 2,283
Posted By KNS
Soon as your data is in table format, I would...

Soon as your data is in table format, I would always suggest you use R for the plotting. Check
http://sekhon.berkeley.edu/stats/html/heatmap.html
More sophisticated next gen packages for R can be...
Forum: Bioinformatics 11-23-2010, 01:01 AM
Replies: 14
Views: 5,393
Posted By KNS
Unstable output from mpileup/samtools

I have observed seemingly unstable outputs from the mpileup using default settings (identical to those suggested in the bowtie and samtools tutorials) and seek suggestions on how to resolve the...
Forum: Bioinformatics 09-08-2010, 12:36 AM
Replies: 10
Views: 4,106
Posted By KNS
Dear Jose, this is brilliant. I will gove it a...

Dear Jose,
this is brilliant. I will gove it a shot - no need to reinvent the wheel. Big thanks for your quick reply!
Forum: Bioinformatics 09-07-2010, 06:07 AM
Replies: 10
Views: 4,106
Posted By KNS
Compile multi-individual SNP tables from bowtie/samtools mappings

I am sure someone must have solved this before, and I wonder if there is not an obviously easy way to do this:

I have GAIIx-RAD data of bowtie-reference-mapped individuals. The resulting...
Forum: Bioinformatics 08-05-2010, 05:14 AM
Replies: 3
Views: 9,949
Posted By KNS
Which commands do you use from within cygwin to...

Which commands do you use from within cygwin to install samtools?
Forum: General 08-04-2010, 05:26 AM
Replies: 0
Views: 1,699
Posted By KNS
Library prep Solid4 paired-end BARCODES

I would like to get several dozen samples individually barcoded before combined Solid 4 sequencing, paired end. Are there any work-arounds to reduce the massive costs associated with barcoding,...
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