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Forum: Academic/Non-Profit Jobs 01-14-2016, 09:52 AM
Replies: 0
Views: 767
Posted By kgulukota
Bioinformatics Post-doc position in the Chicago area

Are you ready to translate your bioinformatics expertise into actual clinical practice? To deploy it in service of actual patient care? If so, this exciting opportunity could be for you.

We are...
Forum: Bioinformatics 01-28-2014, 05:28 AM
Replies: 1
Views: 3,166
Posted By kgulukota
OK. I figured it out - posting here for the...

OK. I figured it out - posting here for the benefit of others who may be in the same predicament.

In the first step, FreeBayes is used to call variants based on sequence called by the basecaller...
Forum: Bioinformatics 01-16-2014, 08:35 AM
Replies: 1
Views: 3,166
Posted By kgulukota
What are the "Flow Evaluator" measures in the Ion Torrent Suite

I am looking at some VCF and bam files generated by Torrent Suite software onboard an Ion Torrent machine (PGM, if that matters).

The VCF has field pairs like the following:

DP - Read Depth
...
Forum: Bioinformatics 10-22-2013, 07:43 AM
Replies: 3
Views: 2,760
Posted By kgulukota
Right. That's what I was afraid of. And I did...

Right. That's what I was afraid of. And I did write some scripts for things I need.

But, when the file is so large everything takes time and I was hoping that some info in an index file can be...
Forum: Bioinformatics 10-22-2013, 06:34 AM
Replies: 3
Views: 2,760
Posted By kgulukota
Can you read VCF.idx?

Is there a way to use VFC.idx file (other than for viewing)?

I have a large (42 Gig) VCF and associated VCF.idx - both generated by GATK. I have some simple questions about this VCF like how many...
Forum: Bioinformatics 08-29-2013, 08:03 AM
Replies: 5
Views: 3,629
Posted By kgulukota
Thank you @dpryan and @swbarnes2. But sorting by...

Thank you @dpryan and @swbarnes2. But sorting by name won't work for me. My project involves examining reads mapped to a particular region - so I have to sort by coordinate in order to load index...
Forum: Bioinformatics 08-28-2013, 12:17 PM
Replies: 5
Views: 3,629
Posted By kgulukota
Can you read a bam file by mate pairs?

I need to process a bam file by reading mate pairs together i.e. each read of the bam file must return TWO alignments to analyze together.

I have been using the Bam API function bam_read_1...
Forum: Bioinformatics 06-21-2013, 01:17 PM
Replies: 2
Views: 1,722
Posted By kgulukota
Re: Create a VCF with your first bam file, say 1.vcf

OK. There is a 3-step procedure that can accomplish what you want (I think).

Step 1. Create VCF's with your first and second bam files separately, say old.vcf and new.vcf.

Step 2. Next...
Forum: Bioinformatics 06-21-2013, 07:55 AM
Replies: 2
Views: 1,722
Posted By kgulukota
I have a similar problem. I get my sequence data...

I have a similar problem. I get my sequence data in batches (not all samples at once) and would like to have a running list of variants called on samples thus far.

As you said, the biggest issue...
Forum: Bioinformatics 04-29-2012, 08:08 PM
Replies: 5
Views: 1,980
Posted By kgulukota
Thank you maubp! I reindexed and it worked...

Thank you maubp!

I reindexed and it worked fine. (The original .bai file was something I downloaded from a public site along with the bam file).
Forum: Bioinformatics 04-28-2012, 06:52 AM
Replies: 5
Views: 1,980
Posted By kgulukota
Thank you twaddlac! Yes, I have been doing...

Thank you twaddlac! Yes, I have been doing something like that. Unfortunately I have multiple files and each file has billions of lines and hence my server takes hours per file for this. I thought...
Forum: Bioinformatics 04-27-2012, 11:43 AM
Replies: 5
Views: 1,980
Posted By kgulukota
Why does samtools idxstats not show the stats

The ref sequences in my bam file are 1, 2, ...

idxstats reports get that 0 reads are mapped to each reference.


$ samtools idxstats MyBam.bam
1 197195432 0 0
10 129993255 0 0...
Forum: Bioinformatics 04-27-2012, 06:20 AM
Replies: 0
Views: 1,031
Posted By kgulukota
ACGT counts from mpileup

I would like to get the counts of A/C/G/T high quality bases aligned at each position from a bam file.

I know that 'samtools mpileup' gives a string with actual read bases and their quality scores...
Forum: Bioinformatics 04-25-2012, 05:38 PM
Replies: 14
Views: 14,142
Posted By kgulukota
That is true seq_lover. Which combinations you...

That is true seq_lover. Which combinations you consider "all good" and which ones "weird" depends on how you constructed your library. Thank you for putting it so succinctly.
Forum: Literature Watch 04-05-2012, 06:44 AM
Replies: 1
Views: 1,208
Posted By kgulukota
Just how much is genetic related anyway?

Roberts et al have analyzed large cohorts of monozygotic twins to try and determine the theoretical limits of how useful genomic sequencing can be.

http://www.ncbi.nlm.nih.gov/pubmed?term=22472521...
Forum: Bioinformatics 02-22-2012, 08:27 AM
Replies: 5
Views: 2,393
Posted By kgulukota
A satisfactory resolution: I have been in...

A satisfactory resolution:

I have been in private correspondence with Ben Langmead. There might be something about my sequence file that is causing great bowtie2 inefficiency. The offending...
Forum: The Pipeline 02-20-2012, 07:02 AM
Replies: 51
Views: 168,463
Posted By kgulukota
Finally! (I am being optimistic and assuming the...

Finally! (I am being optimistic and assuming the legitimate concerns about accuracy will be adequately addressed over time).

I have always thought the true definition of "Next generation" was not...
Forum: Bioinformatics 02-15-2012, 09:06 AM
Replies: 8
Views: 1,329
Posted By kgulukota
Chadn737 - For the pipeline I am building,...

Chadn737 - For the pipeline I am building, mapping to transcripts and to the genome and then combining information from both is important. (I will post more details on it after the pipeline is in a...
Forum: Bioinformatics 02-15-2012, 07:43 AM
Replies: 8
Views: 1,329
Posted By kgulukota
This was to transcripts.

This was to transcripts.
Forum: Bioinformatics 02-15-2012, 07:01 AM
Replies: 8
Views: 1,329
Posted By kgulukota
How do you deal with reads "unmapped to NM_0012345"?

I understand fully what it means when a read is mapped at coordinate X to ref sequence NM_0012345 with a certain quality score etc.

I also understand fully if a read is unmapped (sam flag 4 is...
Forum: Bioinformatics 02-14-2012, 08:55 AM
Replies: 5
Views: 2,393
Posted By kgulukota
I am using beta 5. bowtie2 --version ...

I am using beta 5.

bowtie2 --version
/research/software/Bowtie2/bowtie2-2.0.0-beta5/bowtie2-align version 2.0.0-beta5
64-bit
Built on compute-0-38.local
Thu Dec 15 01:02:29 EST 2011
Compiler:...
Forum: Bioinformatics 02-14-2012, 08:37 AM
Replies: 5
Views: 2,393
Posted By kgulukota
Is bowtie2 really this unstable?

I am having the devil's own time running bowtie2 on a relatively modest set (at most 17 Mill reads) of RNA-seq data.

I run it with the "-a" flag (report all alignments) or a "-k 2" (report 2) or...
Forum: Bioinformatics 02-09-2012, 09:20 AM
Replies: 3
Views: 1,246
Posted By kgulukota
An update: Yes, bowtie2 does have a big issue...

An update:
Yes, bowtie2 does have a big issue with the '-a' flag. I ran bowtie2 on about 8.8 million reads. Following gringer's advice I first ran it with a generous '-k 50' option i.e:

bowtie2...
Forum: Bioinformatics 02-08-2012, 05:54 AM
Replies: 3
Views: 1,246
Posted By kgulukota
Thank gringer! I will try that.

Thank gringer! I will try that.
Forum: Bioinformatics 02-07-2012, 07:39 AM
Replies: 3
Views: 1,246
Posted By kgulukota
Bowtie2 chokes on -a flag?

I am working on project where I need to get ALL hits to each read - defined fairly stringently. I tried to use bowtie2 with a command like this:

bowtie2 --threads 20 --reorder --score-min...
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