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Search: Posts Made By: goutham.atla
Forum: Bioinformatics 01-01-2016, 01:05 PM
Replies: 4
Views: 1,400
Posted By goutham.atla
Yeah. My initial plan was to use freebayes, but...

Yeah. My initial plan was to use freebayes, but it was failing due to memory issues. Erik garrison is looking in to the issue with freebayes.
Forum: Bioinformatics 12-31-2015, 07:34 AM
Replies: 4
Views: 1,400
Posted By goutham.atla
Yes. This is a viral amplicon data, which I would...

Yes. This is a viral amplicon data, which I would expect many variants. The mapping quality is 60, as assigned by the bwa-mem and base qualities are above 30. As I did not mark duplicates, I would...
Forum: Bioinformatics 12-30-2015, 02:48 PM
Replies: 4
Views: 1,400
Posted By goutham.atla
GATK HP is missing high coverage variant sites

I am trying to use GATK HP ( v3.5 ) to call SNPs in amplicon seq data of a small genome of around 600bp. As shown in the attachment, the variants are not called between location 50 and 60, despite...
Forum: Bioinformatics 07-27-2015, 07:06 AM
Replies: 5
Views: 2,154
Posted By goutham.atla
If you want the fasta from BAM file, I don't...

If you want the fasta from BAM file, I don't think so there is any tool. But what could you do is to get the reads mapped to regions of interests using samtools with -L option and then try to merge...
Forum: Bioinformatics 07-27-2015, 06:57 AM
Replies: 2
Views: 1,596
Posted By goutham.atla
cor() function in R should be able to do that.

cor() function in R should be able to do that.
Forum: RNA Sequencing 04-21-2014, 03:07 PM
Replies: 1
Views: 1,584
Posted By goutham.atla
miRNA alignment

Hi all,

I have not done miRNA data analysis before, I have a small question regarding miRNA read mapping. The miRNAs are generated either by cleaving off from a mRNA or from a translated hairpin...
Forum: Bioinformatics 04-10-2014, 09:11 PM
Replies: 1
Views: 1,015
Posted By goutham.atla
cufflinks with GTF file

Hi,

If we are not looking for novel isoforms, we need to use GTF file with cufflinks ( -G GTF ).

My question is that if we do not want any novel isoforms, we can skip the cufflinks step in...
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