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Forum: Academic/Non-Profit Jobs 02-17-2018, 08:21 PM
Replies: 0
Views: 373
Posted By shurjo
early-career bioinformatician opportunity at NIH

The Cancer Immunobiology Section at the National Cancer Institute is looking for a talented early-career bioinformatician to join a team of scientists in Bethesda, MD doing groundbreaking work...
Forum: Bioinformatics 10-29-2015, 09:25 AM
Replies: 0
Views: 1,222
Posted By shurjo
strand-specificity in RSEM

Hello,

I'm trying to figure out the settings for analysing strand-specific RNA-Seq data from Illumina TruSeq chemistry with rsem-calculate-expression

Specifically, regarding the...
Forum: Bioinformatics 09-24-2012, 06:52 PM
Replies: 5
Views: 878
Posted By shurjo
All of these sound very logical. I'm going to...

All of these sound very logical. I'm going to step out of my TopHat-based comfort zone and try STAR and SOAP3-dp.

ECO, nice to see the forum doing so well. I've been away from this world for a bit...
Forum: Bioinformatics 09-24-2012, 03:16 PM
Replies: 5
Views: 878
Posted By shurjo
running TopHat with ~1.2 billion reads

Any tips for the quickest way to get TopHat to complete alignment of a very large dataset (~1.2 billion 75bp Single end HiSeq reads)? I considered splitting it into 10 but then realized this would...
Forum: Bioinformatics 03-27-2012, 03:39 PM
Replies: 32
Views: 29,334
Posted By shurjo
Hi Karel, Thanks for the tips. They worked...

Hi Karel,

Thanks for the tips. They worked for me as well.

Regards,

Shurjo
Forum: Bioinformatics 03-26-2012, 09:40 PM
Replies: 32
Views: 29,334
Posted By shurjo
Hi Loyal, I'm facing the same situation as...

Hi Loyal,

I'm facing the same situation as kareldegendt.

Can you provide a set of instructions for upgrading to a newer version when cummerRbund is already on a system (64-bit Linux)? This...
Forum: Bioinformatics 03-26-2012, 03:14 PM
Replies: 3
Views: 2,398
Posted By shurjo
getSig function in cummerBund

Hi CummeRbund authors,

Is there a known bug which causes getSig to be unavailable even if CummerBund installed properly?
> library(cummeRbund)
> getSig()
Error: could not find function "getSig"...
Forum: Bioinformatics 10-24-2011, 08:46 AM
Replies: 17
Views: 14,068
Posted By shurjo
Look here:...

Look here: http://cufflinks.cbcb.umd.edu/igenomes.html
Forum: Bioinformatics 09-27-2011, 01:59 PM
Replies: 2
Views: 2,313
Posted By shurjo
I've used coevrageBed from BedTools for this and...

I've used coevrageBed from BedTools for this and negative percentages sounds somewhat surprising. Can you post the syntax you used on the command line and maybe a short section from your output file?
Forum: Sample Prep / Library Generation 07-19-2011, 06:32 PM
Replies: 8
Views: 4,011
Posted By shurjo
So would I!

So would I!
Forum: Sample Prep / Library Generation 07-14-2011, 01:38 PM
Replies: 2
Views: 2,690
Posted By shurjo
Pippin Prep vs. gel elution for RNA-Seq

I had a chance to do a side-by-side comparison of Pippin Prep (PP) and agarose gels (AG) for size selection during RNA-Seq library prep and would like to share these results with the community and...
Forum: Sample Prep / Library Generation 07-11-2011, 08:03 AM
Replies: 11
Views: 2,621
Posted By shurjo
I used the DynaBeads kit from Invitrogen with 2...

I used the DynaBeads kit from Invitrogen with 2 rounds of purification. mRNA yield from 10ug of total RNA with RIN=10 was about 120ng.

HTH,

Shurjo
Forum: Sample Prep / Library Generation 07-08-2011, 01:12 PM
Replies: 2
Views: 3,454
Posted By shurjo
Thanks ECO! Will try this out and post again once...

Thanks ECO! Will try this out and post again once I have the results.
Forum: Sample Prep / Library Generation 07-08-2011, 10:17 AM
Replies: 3
Views: 1,038
Posted By shurjo
I would definitely go with PE as that is the...

I would definitely go with PE as that is the general direction RNA-Seq data analysis software seems to be taking. In the first year or so after RNA-Seq was introduced, PE data was generally just...
Forum: Sample Prep / Library Generation 07-08-2011, 09:57 AM
Replies: 2
Views: 1,810
Posted By shurjo
I've been making RNA-Seq libraries for three...

I've been making RNA-Seq libraries for three years now, basically following the same protocol as one of the first papers (Marioni et al 2008) with a few modifications (e.g RNA fragmentation on...
Forum: Sample Prep / Library Generation 07-08-2011, 07:15 AM
Replies: 11
Views: 2,621
Posted By shurjo
I'm attaching a picture from poly(A)-selected...

I'm attaching a picture from poly(A)-selected mRNA (from 10ug of total RNA) run on a Pico Chip. As you can see, the ribosomal molecules are still noticeably present, but then those are very hard to...
Forum: Sample Prep / Library Generation 07-07-2011, 08:08 PM
Replies: 2
Views: 3,454
Posted By shurjo
removal of primer dimers.

I'm trying to tweak the Illumina RNA-Seq library prep to convert a library of blunt-ended PCR amplicons (sized between 200-600bp) into sequencer-ready form. The starting material is in the low...
Forum: Bioinformatics 07-07-2011, 06:24 PM
Replies: 7
Views: 1,468
Posted By shurjo
Agreed. Maybe we will get a better insight after...

Agreed. Maybe we will get a better insight after camelbbs looks at the actual BAM file to see what's in it.

Another option would be to run FastQC on the input file to check the quality of the...
Forum: Bioinformatics 07-07-2011, 01:08 PM
Replies: 7
Views: 1,468
Posted By shurjo
This is absolutely normal. accepted_hits.bam is...

This is absolutely normal. accepted_hits.bam is in the binary BAM format which uses much less space than fastq (which is in text format).
Forum: Bioinformatics 06-14-2011, 06:51 PM
Replies: 1
Views: 3,578
Posted By shurjo
Look here...

Look here (http://cufflinks.cbcb.umd.edu/howitworks.html#reps) for an answer.
Forum: Bioinformatics 06-11-2011, 09:32 AM
Replies: 3
Views: 1,830
Posted By shurjo
Thanks! It's very generous of you to share your...

Thanks! It's very generous of you to share your code with the community.
Forum: Introductions 06-06-2011, 10:09 AM
Replies: 10
Views: 4,606
Posted By shurjo
Sure, pm me your email ID.

Sure, pm me your email ID.
Forum: Introductions 06-05-2011, 02:12 PM
Replies: 10
Views: 4,606
Posted By shurjo
Each "platform" (Illumina/Solid/454/PacBio) can...

Each "platform" (Illumina/Solid/454/PacBio) can be used for multiple "techniques" (whole-genome/exome/transcriptome/ChipSeq/custom application). An analogous word sometimes used for "platform" is...
Forum: Bioinformatics 06-04-2011, 09:35 PM
Replies: 1
Views: 2,243
Posted By shurjo
What comes after cuffdiff?

I guess this is a pretty open-ended question, but maybe the community will have some interesting discussions on it, so I'm throwing it out all the same. The dilemma I'm facing: I ran the...
Forum: Bioinformatics 06-04-2011, 07:53 PM
Replies: 14
Views: 3,616
Posted By shurjo
Under normal circumstances no trimming should be...

Under normal circumstances no trimming should be needed as the adapters are not part of the read (they contain the binding sites for the sequencing primers, hence the actual read starts after the...
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