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Forum: RNA Sequencing 03-09-2016, 10:54 AM
Replies: 4
Views: 2,398
Posted By N00bSeq
It must be something more fundamental that I'm...

It must be something more fundamental that I'm doing wrong here. Now I also tried to make use of the info on https://sourceforge.net/p/mageck/wiki/Home/, up to the part about trimming:

I...
Forum: RNA Sequencing 03-09-2016, 10:34 AM
Replies: 4
Views: 2,398
Posted By N00bSeq
You are right. That was an issue. I instead tried...

You are right. That was an issue. I instead tried trimming a fix number of bases from the 5' end with another tool


seqtk trimfq -b 30 SRR2071309.fastq > SRR2071309.setk.trimmed.fastq


Then...
Forum: RNA Sequencing 03-09-2016, 08:23 AM
Replies: 4
Views: 2,398
Posted By N00bSeq
Help with mapping sgRNA reads from CRISPR/Cas9 screen

Hi!

I am somewhat of a beginner and will soon receive data from a CRISPR-screen, and would like to get familiar with the workflow. For now, I am trying to map and normalize reads from public data....
Forum: Bioinformatics 05-16-2014, 05:51 AM
Replies: 5
Views: 1,982
Posted By N00bSeq
I don't really know why this happens (It does in...

I don't really know why this happens (It does in my data as well. I suspect it is influenced by library construction method and any adapter and rRNA contamination that may be present.). But here is...
Forum: Bioinformatics 05-14-2014, 02:07 AM
Replies: 32
Views: 18,858
Posted By N00bSeq
I am getting the same error (fail when reporting...

I am getting the same error (fail when reporting output tracks) on tophat 2.0.11. I have made three mapping runs for each of 12 samples. Of these, only the ones using both --no-discordant and...
Forum: Bioinformatics 05-09-2014, 07:13 AM
Replies: 14
Views: 2,402
Posted By N00bSeq
OK, thank you for clarifying. In order to get the...

OK, thank you for clarifying. In order to get the fragment length I would then add 2*100, yielding an average fragment size of 170. This is less than the sum of the read lengths (2*100), and thus the...
Forum: Bioinformatics 05-09-2014, 06:22 AM
Replies: 14
Views: 2,402
Posted By N00bSeq
You may be right. The company in question did at...

You may be right. The company in question did at first make a false claim that the library preparation method they used was not strand specific (which I have later confirmed it to be), so I would not...
Forum: Bioinformatics 05-09-2014, 05:59 AM
Replies: 14
Views: 2,402
Posted By N00bSeq
I'm pretty sure fragmentation was done, just no...

I'm pretty sure fragmentation was done, just no size selection on those fragments.
Forum: Bioinformatics 05-09-2014, 05:21 AM
Replies: 14
Views: 2,402
Posted By N00bSeq
Is there any way of turning off this feature? I...

Is there any way of turning off this feature? I noticed the options

--no-effective-length-correction

and

--no-length-correction

in the cufflinks manual, which may or may not do this....
Forum: Bioinformatics 04-24-2014, 07:14 AM
Replies: 3
Views: 2,056
Posted By N00bSeq
I am also curious about this. Running cuffcompare...

I am also curious about this. Running cuffcompare on my cuffmerge output results in these numbers:


# Query mRNAs : 865356 in 787440 loci (97791 multi-exon transcripts)
# ...
Forum: Bioinformatics 04-24-2014, 05:12 AM
Replies: 0
Views: 912
Posted By N00bSeq
Question Cuffcompare fails to properly match reference to itself

I have stumbled upon something that I consider really strange.

I ran cuffcompare (2.2.0) on the Ensembl mouse reference annotation from igenomes (NCBI37, May 14 22:13), using both the same...
Forum: Bioinformatics 04-24-2014, 04:07 AM
Replies: 2
Views: 1,490
Posted By N00bSeq
I suspect this may be related to cuffcompare...

I suspect this may be related to cuffcompare excluding "contained" transcripts. Maybe using the -C flag will give less mysterious results.

From the manual:
"-C Enables the "contained"...
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