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Forum: Bioinformatics 03-17-2017, 07:11 AM
Replies: 2
Views: 1,865
Posted By komalsrathi
tophat-fusion-post: ValueError: invalid literal for int() with base 10: 'exonCount'

Hi everyone,

I am running tophat-fusion-post like this:

tophat-fusion-post -o ./fusion_results -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5...
Forum: Bioinformatics 10-08-2015, 11:36 AM
Replies: 0
Views: 1,978
Posted By komalsrathi
STAR Aligner Output BAM Processing

Hi everyone,

I am a new user of STAR Aligner. I have been using GSNAP until now, but my new group likes STAR better. I am very excited about using it and have a couple of questions too. We will be...
Forum: RNA Sequencing 06-02-2014, 10:43 AM
Replies: 0
Views: 2,482
Posted By komalsrathi
Warning in CuffDiff when using novel transcripts from CuffMerge as input

Hi everyone,

I am doing a differential gene expression test on RNASeq data from 64 Human Heart samples as follows:

cufflinks --library-type fr-firststrand -p 2 -o cufflinks_out <bam_file>
...
Forum: Bioinformatics 11-27-2013, 09:09 AM
Replies: 1
Views: 3,565
Posted By komalsrathi
Cuffmerge output with missing strand information, htseq-count error

Hi everyone,

I used cuffmerge to obtain a merged.gtf file but there are 3700 entries in my merged.gtf file that contain '.' in the strand field instead of '+' or '-'. I checked the entries that do...
Forum: Bioinformatics 11-22-2013, 12:29 PM
Replies: 1
Views: 4,718
Posted By komalsrathi
mpileup to vcf

Hi everyone,

I know there is a perl script 'sam2vcf.pl' to convert a pileup file to .vcf format. But I wanted to know whether there is any tools/script that converts mpileup format to .vcf format...
Forum: Bioinformatics 11-19-2013, 12:30 PM
Replies: 4
Views: 2,729
Posted By komalsrathi
The issue is solved. I parsed my alignments to...

The issue is solved. I parsed my alignments to remove any alignment matching '\t\*\t' pattern. Thanks
Forum: Bioinformatics 11-04-2013, 12:03 PM
Replies: 4
Views: 2,729
Posted By komalsrathi
Hi Simon, I updated htseq-count to version...

Hi Simon,

I updated htseq-count to version 0.5.4p5 and now I am getting a different error but for the same file:



This is line no. 50956571. As you can see it contains only Ns.
...
Forum: Bioinformatics 10-28-2013, 06:04 AM
Replies: 4
Views: 2,729
Posted By komalsrathi
Hi Simon, I am using "Part of the 'HTSeq'...

Hi Simon,

I am using "Part of the 'HTSeq' framework, version 0.5.4p1". I will update it to the latest version. Thanks for the prompt reply.
Forum: Bioinformatics 10-24-2013, 10:25 AM
Replies: 4
Views: 2,729
Posted By komalsrathi
Error in HTSEQ

Hi everyone,

I am using the latest version of GSNAP to get alignments for 29 RNAseq samples. So after I get a SAM alignment from GSNAP, I use samtools to convert it into BAM and then:



...
Forum: Bioinformatics 09-12-2013, 12:22 PM
Replies: 2
Views: 1,912
Posted By komalsrathi
I know, I just can't find a delete option for...

I know, I just can't find a delete option for this post!
Forum: Bioinformatics 09-12-2013, 08:36 AM
Replies: 2
Views: 1,912
Posted By komalsrathi
Get random alignments from SAM file

Hi all,

I have a .sam file and I want to extract random alignments from it.

I googled a bit and there are quite a few tools that have commands to "downsample a sam file" like Picard and GATK....
Forum: Bioinformatics 08-06-2013, 09:30 AM
Replies: 2
Views: 22,545
Posted By komalsrathi
Oh thanks! My fasta file was in a directory...

Oh thanks!
My fasta file was in a directory which required permission for writing onto.
I was running the command from a separate directory and assumed the new file would be created in this...
Forum: Bioinformatics 08-06-2013, 09:15 AM
Replies: 2
Views: 22,545
Posted By komalsrathi
creating .fai from .fa file using samtools faidx command

Hi everyone,

I am trying to create a FASTA index from a FASTA file using samtools:

./samtools faidx /home/krathi/data/ChIPseq/mm9/mm9.fa

but it shows me the error:

[fai_build] fail to...
Forum: Bioinformatics 08-06-2013, 09:06 AM
Replies: 4
Views: 1,988
Posted By komalsrathi
New to the forum

how do I create a new thread?
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