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Forum: Bioinformatics 10-28-2014, 07:57 AM
Replies: 4
Views: 2,297
Posted By bbl
Thanks very much kmcarr. Indeed what you...

Thanks very much kmcarr. Indeed what you suspected is what happens!
1st, CEBPA is the gene I'm intereted. From samout by HTSeq-count, reads are mapped to two and three different genes incl. CEBPA....
Forum: Bioinformatics 10-28-2014, 07:51 AM
Replies: 4
Views: 2,297
Posted By bbl
Thanks very much dpryan. I shall try...

Thanks very much dpryan. I shall try featureCounts too.
Forum: Bioinformatics 10-28-2014, 03:22 AM
Replies: 4
Views: 2,297
Posted By bbl
samtools sorting issue or HTSeq-count problem?

Hello all,

This has puzzled me for days and I couldnt find any explanation on the internet.
I noticed HTSeq-count gives the reads counts of a gene as 0. But when viewed in IGV with the...
Forum: Bioinformatics 06-19-2014, 05:57 AM
Replies: 3
Views: 2,738
Posted By bbl
Thanks kmcarr- my ignorance, didnt remember htseq...

Thanks kmcarr- my ignorance, didnt remember htseq counts the pair-read only once. Nevertheless, is it reasonable to have 57% of mapped read-pairs for DE analysis? It seems to me still quite a lot...
Forum: Bioinformatics 06-19-2014, 02:17 AM
Replies: 3
Views: 2,738
Posted By bbl
Question What is wrong with merely 28% tophat2 mapped reads are counted by HTSeq-count

Here is how my data has been processed: 150bp PE RNAseq, trimmed, tophat2 mapped on both transcriptome and genome using default setting apart from insert-size and std (calculated from sampling), then...
Forum: Bioinformatics 11-15-2013, 05:53 AM
Replies: 27
Views: 17,418
Posted By bbl
Thanks Simon. Does it mean I can understand that...

Thanks Simon. Does it mean I can understand that I only need to filter multiple mapped reads in the accepted_hits.bam from tophat2? No other filtering step necessary prior to HTseq-count?
Forum: Bioinformatics 11-13-2013, 03:55 AM
Replies: 27
Views: 17,418
Posted By bbl
How does HTseq-count count paired-end reads which...

How does HTseq-count count paired-end reads which are mapped on different chromosomes or genes? Or should they be filtered out prior htseq-count run?
Forum: RNA Sequencing 10-04-2013, 06:32 AM
Replies: 5
Views: 2,858
Posted By bbl
I am not too bothered with the first 15bp as we...

I am not too bothered with the first 15bp as we all know why. For the rest of the read length, the difference between AT and GC is small although they are not exact 25% each. Does it look acceptable...
Forum: RNA Sequencing 10-04-2013, 04:58 AM
Replies: 5
Views: 2,858
Posted By bbl
I also have similar problem with base composition...

I also have similar problem with base composition with the PE RNA-seq data I was given. Even the mapped reads still have this problem. I wonder if it has something to do with the lib prep kit? We...
Forum: Bioinformatics 11-18-2010, 04:09 AM
Replies: 3
Views: 1,370
Posted By bbl
It seems to me that how many bp to shift the...

It seems to me that how many bp to shift the reads are crucial for identifying the TFBS. Since different parameters give such a dramatic different L, I am not very confident for downstream TFBS...
Forum: General 11-18-2010, 01:44 AM
Replies: 3
Views: 1,734
Posted By bbl
Pymol, VMD and Rasmol all can do what you want...

Pymol, VMD and Rasmol all can do what you want quite straight forward. I am afraid that I never used Cn3D before, so cannot help you with that,
Forum: Bioinformatics 11-18-2010, 01:19 AM
Replies: 3
Views: 1,370
Posted By bbl
any suggestions from who have experience with...

any suggestions from who have experience with CisGenome?
Forum: Bioinformatics 11-17-2010, 02:45 AM
Replies: 3
Views: 1,370
Posted By bbl
shifting reads in cisgenome for chip-seq 2-sample analysis

Hello there,

I am following the cisgenome online tutorial for 2-sample chip-seq analysis. I compare the median of peak length calculated from hts_peakdetectorv2_2sample -br 0 -ssf 0 and -br 1 -brl...
Forum: Bioinformatics 10-27-2010, 07:02 AM
Replies: 0
Views: 1,988
Posted By bbl
Install spp (chip-seq processing pipeline)

Hello there,

I am trying to install spp but of course it doesn't work! There is no information on http://compbio.med.harvard.edu/Supplements/ChIP-seq/ about what compiler or library or...
Forum: Bioinformatics 09-07-2010, 05:57 AM
Replies: 191
Views: 70,393
Posted By bbl
Hello Simon, HTSeq seems to be the right...

Hello Simon,

HTSeq seems to be the right tool I need for my work. I am trying to count how many times each base in an interesting region of exon has been covered by a read. Can 'counting' function...
Forum: Bioinformatics 09-06-2010, 11:58 AM
Replies: 4
Views: 4,285
Posted By bbl
Hello there, I recently have encoutered the...

Hello there,
I recently have encoutered the same problem. Have you got it sorted? Perhaps, you can divulge a bit information... thanx
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