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Forum: Illumina/Solexa 11-19-2015, 04:18 PM
Replies: 58
Views: 50,084
Posted By son_nexg
Hi Guys I did a tophat2 alignment of the...

Hi Guys

I did a tophat2 alignment of the stranded RNA-seq data generated with Trueseq libraries and I am getting strange/random distribution of the reads between sense and antisense strand:

...
Forum: Bioinformatics 06-19-2013, 11:06 PM
Replies: 21
Views: 40,656
Posted By son_nexg
Hi all, I ran into a problem while using the...

Hi all,

I ran into a problem while using the cuffmerge. A transcript of my interest was their in three individual cufflinks assemblies (.gtf) but it got lost when I merged them using the...
Forum: Bioinformatics 09-13-2011, 08:25 PM
Replies: 5
Views: 4,272
Posted By son_nexg
Thanks for your reply 'robs'. I will have a...

Thanks for your reply 'robs'.

I will have a look at the literature on this.
I was just wondering about it ... so far I was dealing with the DNA seq data and I would expect roughly 10% duplicates...
Forum: Bioinformatics 09-13-2011, 08:00 PM
Replies: 5
Views: 4,272
Posted By son_nexg
Hi Just to add to the above question - Could...

Hi Just to add to the above question - Could estimate amount of PCR duplication in the RNA-seq data ?

Thank you!
Forum: Bioinformatics 09-13-2011, 04:23 PM
Replies: 21
Views: 12,651
Posted By son_nexg
Thanks a lot, -Q option worked for me!! I am...

Thanks a lot, -Q option worked for me!!

I am now onto the next step and generating the nucleotide distribution graph by doing:

fastx_nucleotide_distribution_graph.sh \
-i...
Forum: Bioinformatics 09-12-2011, 09:35 PM
Replies: 21
Views: 12,651
Posted By son_nexg
Hi guys, I want to use 'fastx_quality_stats'...

Hi guys,

I want to use 'fastx_quality_stats' for my illumina data but it gives the following error:

fastx_quality_stats -i /PATH/Sample_XX.fastq -o /PATH/Sample_xx.fastq.stats...
Forum: Bioinformatics 09-12-2011, 07:02 PM
Replies: 22
Views: 8,861
Posted By son_nexg
Hi I am experiencing problems using .sam output...

Hi I am experiencing problems using .sam output by Tophat with Cufflink.
My first question is : What options should I use to generate a .bam file with Tophat ?

If thats not possible, could...
Forum: RNA Sequencing 07-26-2011, 08:22 PM
Replies: 3
Views: 2,731
Posted By son_nexg
Has anyone tried Cufflink for de novo assembly of...

Has anyone tried Cufflink for de novo assembly of bacterial transcript ? If yes, I would be interested in knowing how it went and results obtained :)

Does anyone have an idea about coverage/depth...
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