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Forum: Bioinformatics 07-13-2012, 01:56 PM
Replies: 2
Views: 3,767
Posted By manianslab
@liueagle, it appears that since bowtie2 by...

@liueagle, it appears that since bowtie2 by default allows less stringent matching (e.g. gaps), the number of mapped reads is higher, but tophat perhaps checks them and makes sure they meet the...
Forum: Bioinformatics 07-02-2012, 10:15 AM
Replies: 7
Views: 3,723
Posted By manianslab
I had to delete some lines from a file once like...

I had to delete some lines from a file once like this. I used the sed command. See this thread:...
Forum: Bioinformatics 06-29-2012, 02:32 PM
Replies: 16
Views: 7,300
Posted By manianslab
Okay, here is my attempt at a qucik perlscript to...

Okay, here is my attempt at a qucik perlscript to do this (see attachment). Hope some perl expert can make it less clumsy!
Forum: Bioinformatics 06-29-2012, 01:29 PM
Replies: 16
Views: 7,300
Posted By manianslab
Unfortunately, cuffdiff does not seem to carry...

Unfortunately, cuffdiff does not seem to carry over the original transcript ids from the merged.gtf file in to the output files. However, you can either use Excel (vlookup) or a perlscript or awk to...
Forum: Bioinformatics 06-27-2012, 02:59 PM
Replies: 0
Views: 1,105
Posted By manianslab
cufflinks-2.0.x take much longer than cufflinks-1.0.3 for assembly??

I was just checking the new cufflinks versions (2.0.0 and now 2.0.1) with a test dataset. The recent versions appear to take way too long to build the gtf files compared to the old version. Anyone...
Forum: Bioinformatics 06-27-2012, 02:41 PM
Replies: 2
Views: 1,555
Posted By manianslab
Read the manual carefully. -G would not build...

Read the manual carefully. -G would not build novel transcripts (novels genes/isoforms) if any found using your RNA Seq reads where as -g would. So depends on what you want.
Forum: Bioinformatics 06-26-2012, 06:44 AM
Replies: 2
Views: 1,788
Posted By manianslab
@cedance: Thanks for your response. My post...

@cedance: Thanks for your response. My post perhaps was not clear. After the cufflinks run, we use cuffmerge to generate merged gtf and then run cuffdiff on it on each of our bam files. But, I see...
Forum: Bioinformatics 06-25-2012, 02:49 PM
Replies: 2
Views: 1,788
Posted By manianslab
How to use cufflinks only to assemble transcripts, but not estimate abundance?

We use the tophat-cufflinks-cuffmerge-cuffdiff pipeline for RNA Seq analysis. I am wondering if there is a way to have "cufflinks" - the command not the package - just do the transcript assembly...
Forum: Bioinformatics 06-21-2012, 02:37 PM
Replies: 2
Views: 3,767
Posted By manianslab
tophat2/bowtie2 inconsistency in number of unmapped reads

We are using the tophat-cufflinks pipeline for RNA seq. With tophat1-bowtie1 mapping, the reads are mapped initially to the predicted transcriptome and then unmapped reads are mapped to the genome to...
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