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Forum: Bioinformatics 05-13-2013, 02:50 PM
Replies: 3
Views: 899
Posted By jkozubek
I think so too. Still it seems odd that the...

I think so too. Still it seems odd that the distribution is lopsided so that many more times its the ALT that is seen in only 20-30% in the reads.
Forum: Bioinformatics 05-13-2013, 02:37 PM
Replies: 3
Views: 899
Posted By jkozubek
Allele Distributions

Hello:

I found 320 mutations among 16 mouse clones using GATK. However, I noticed something strange. In only 40 of those 0/1 calls are there more reads with the ALT call (1) than reads with the...
Forum: Bioinformatics 09-28-2012, 09:35 AM
Replies: 2
Views: 2,342
Posted By jkozubek
Mouse (MM10) SNPs

Hello,

Does anyone know if there is a VCF file of SNPs and Indels available yet for MM10 (mouse), and where to obtain it?

I need this for GATK.

Jim
Forum: Bioinformatics 09-10-2012, 09:16 AM
Replies: 3
Views: 2,418
Posted By jkozubek
Sequencer is coding in Sanger/Illumina 1.9 (ASCii...

Sequencer is coding in Sanger/Illumina 1.9 (ASCii + 33) scale. I noticed BWA recoded the values by subtracting 33. So it adjusted all the base calls. I checked and the base calls are -33 in the BWA...
Forum: Bioinformatics 09-10-2012, 06:26 AM
Replies: 3
Views: 2,418
Posted By jkozubek
This was not the answer. In fact, upon further...

This was not the answer.
In fact, upon further investigation, I discovered the sequence data we received has very low base quality. I set samtools mpileup to -Q 0 and now get lots of SNPs.
Forum: Bioinformatics 09-08-2012, 01:49 PM
Replies: 3
Views: 2,418
Posted By jkozubek
I believe I did not specify -I parameter in bwa...

I believe I did not specify -I parameter in bwa to specify Illumina 1.3+ ASCII
Forum: Bioinformatics 09-08-2012, 12:44 PM
Replies: 3
Views: 2,418
Posted By jkozubek
SAMTOOLS mpileup only INDELs, no SNPs?

Hi All,

I used BWA to create BAM files. Then I used samtools mpileup to create a VCF file. However, there were only indels (no SNPs) in my VCF file.

Right now, I am using samtools fillmd to...
Forum: Bioinformatics 11-16-2011, 10:46 AM
Replies: 1
Views: 1,452
Posted By jkozubek
Nevermind. i will use a different version.

Nevermind. i will use a different version.
Forum: Bioinformatics 11-16-2011, 09:54 AM
Replies: 1
Views: 1,452
Posted By jkozubek
BWA No BAM Input Option?

Hi: This might be an easy question. I am using the new BWA-0.5.9 version, and there doesn't seem be a -b option for alignments to specify BAM file format as input. Does anyone know if it still...
Forum: Bioinformatics 07-27-2011, 05:40 AM
Replies: 2
Views: 6,388
Posted By jkozubek
Thanks for comments!

Thanks for comments!
Forum: Bioinformatics 07-26-2011, 11:10 AM
Replies: 2
Views: 6,388
Posted By jkozubek
Tophat - Left Kept Reads

Hello:

I am wondering if Tophat generates a file of seq direct to the genome, prior to doing its mapping to the exon-exon junctions. I am hoping it does, such that i don't need to do a separate...
Forum: Bioinformatics 07-14-2011, 01:52 PM
Replies: 4
Views: 2,187
Posted By jkozubek
Structural Variants

Hello all:

I interested in what tools people have found easiest and useful for detection of structural variants (including indels, inversions, translocations).

Jim
Forum: Bioinformatics 03-14-2011, 06:25 PM
Replies: 13
Views: 5,862
Posted By jkozubek
Nevermind. i see from my output that it is...

Nevermind. i see from my output that it is mapping reads under the min read length.
Forum: Bioinformatics 03-14-2011, 05:14 PM
Replies: 13
Views: 5,862
Posted By jkozubek
Does anyone know if Tophat is therefore ignoring...

Does anyone know if Tophat is therefore ignoring reads less than the min read length? For instance, if it sets min read length at 20 bp and max read length at 26 bp, would it ignore mapping of a read...
Forum: Bioinformatics 03-11-2011, 06:47 AM
Replies: 8
Views: 2,260
Posted By jkozubek
Thats what i was thinking but it said i am...

Thats what i was thinking but it said i am required to input an -r value. i guess i can just set it to 0.
Forum: Bioinformatics 03-10-2011, 07:37 PM
Replies: 8
Views: 2,260
Posted By jkozubek
I used parafin archived samples for sequencing...

I used parafin archived samples for sequencing and all of my RNA is in very tiny bits < 30 bp. Can you suggest an -r setting that would be appropriate for Tophat?
Forum: Bioinformatics 03-07-2011, 06:54 PM
Replies: 8
Views: 2,260
Posted By jkozubek
I am working on Tophat. Do you know if Tophat...

I am working on Tophat. Do you know if Tophat maps normal reads inside exons as well as mapping exon-exon junction reads?

Then, looks like i will have to write a script to compare the Tophat...
Forum: Bioinformatics 03-05-2011, 06:19 PM
Replies: 8
Views: 2,260
Posted By jkozubek
Question RNA biotypes

Hello:

This is my first post.

I am a genetics student at UConn. I have Illumina RNA-Seq data and my PI wants me to determine the RNA distribution (tRNA%, rRNA%, snoRNA%). I already determined...
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