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Forum: Bioinformatics 02-23-2015, 06:20 AM
Replies: 10
Views: 10,454
Posted By amolkolte
Hello All, I was having this issue, while I...

Hello All,

I was having this issue, while I was running "cuffmerge" on the assemblies built using cufflinks 2.1.1.

It turned out, that the problem with duplicated entries was not with the...
Forum: RNA Sequencing 02-23-2015, 06:17 AM
Replies: 11
Views: 10,170
Posted By amolkolte
Dear All, I was having this issue, while I...

Dear All,

I was having this issue, while I was running "cuffmerge" on the assemblies built using cufflinks 2.1.1.

I checked in my reference gtf if the duplicated entry exists but there wasn't...
Forum: Bioinformatics 01-20-2015, 09:10 AM
Replies: 218
Views: 146,449
Posted By amolkolte
saturate the junctions!!

Hi,
Would it be wise to generate the genome with GTF file and re-generate it later with the sample specific SJ.out.tab?

I have more than 100 samples for variant analysis. Another strategy that I...
Forum: Bioinformatics 04-03-2014, 11:41 PM
Replies: 2
Views: 2,690
Posted By amolkolte
InterProScan followed by BiNGO

blast2go is on the verge of getting commercialized (as they have started selling PRO versions) and my previous experience was not so good with it. I used IntrProScan to associate GO terms with the...
Forum: RNA Sequencing 01-29-2013, 02:07 AM
Replies: 22
Views: 14,720
Posted By amolkolte
Thumbs down After running for 6 days, gsnap finally generated...

After running for 6 days, gsnap finally generated an 34 GB sam file.

Alternatively, I noticed at later point that you can monitor the output file size under your 'gsnap_out' directory and estimate...
Forum: Bioinformatics 01-24-2013, 01:57 AM
Replies: 36
Views: 19,299
Posted By amolkolte
Thanks TheRob and Stroehli !! TheRob - I was...

Thanks TheRob and Stroehli !!

TheRob - I was using transbyss for de-novo assembly, since I don't have a concrete reference to begin with.

Stroehli - I have used abyss to assemble the contigs....
Forum: RNA Sequencing 01-24-2013, 01:42 AM
Replies: 22
Views: 14,720
Posted By amolkolte
I have been running GSNAP as a part of trinity...

I have been running GSNAP as a part of trinity pipeline.

To begin with, I have paired ends reads of 7GB of size for each read file.
The pipeline has executed the following code,


gsnap -d...
Forum: Bioinformatics 12-10-2012, 10:00 PM
Replies: 36
Views: 19,299
Posted By amolkolte
I have the raw FASTQ reads and in order to...

I have the raw FASTQ reads and in order to perform de novo assembly using transAbySS, I need to feed the input in the form of bam or sam. Can you please shed some light on this.
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