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Search: Posts Made By: KamilSJaron
Forum: Bioinformatics 07-19-2016, 12:44 AM
Replies: 6
Views: 2,886
Posted By KamilSJaron
Brian, yes, I guess so, given the fraction of...

Brian, yes, I guess so, given the fraction of short insert sizes with convergent orientation. There reads were trimmed (and qc looked good), therefore I expected that the facrtion of short inserts is...
Forum: Bioinformatics 07-18-2016, 03:52 PM
Replies: 6
Views: 2,886
Posted By KamilSJaron
You are right. Twice. Mate-pair indeed...

You are right. Twice.

Mate-pair indeed should, be pointing out from each other, but this is not the problem. And here comes, why you were right twice - bowtie thought that I have pair-end reads,...
Forum: Bioinformatics 07-18-2016, 11:06 AM
Replies: 6
Views: 2,886
Posted By KamilSJaron
Cheers Ryan! Yes, these are mate-pairs...

Cheers Ryan!

Yes, these are mate-pairs (That is why I expected this insert size). Is it really important for mapper to know that the library is mate-pair library? It is already post-processed -...
Forum: Bioinformatics 07-18-2016, 08:55 AM
Replies: 6
Views: 2,886
Posted By KamilSJaron
Lightbulb bowtie2 bit 2 of the flag

Hello,

I am wondering what does mean "The second bit (2 in decimal, 0x2 in hexadecimal) is set if the read is part of a pair that aligned in a paired-end fashion."

I have mate pair reads mapped...
Forum: Pacific Biosciences 07-12-2016, 08:35 AM
Replies: 7
Views: 4,540
Posted By KamilSJaron
Hello guys, I am very happy to see this...

Hello guys,

I am very happy to see this thread. How do you specify a number of concurrent jobs on local computer / number of cores / memory falcon can use at most???

I mean, I see that...
Forum: Bioinformatics 07-12-2016, 07:52 AM
Replies: 1
Views: 3,179
Posted By KamilSJaron
I wrote a small python script for conversion of...

I wrote a small python script for conversion of .sam produced by kallisto to .sam readable by IGV using .gtf file. It is not perfect (I was bit in rush when I was writing it) and all transctipts on...
Forum: Bioinformatics 04-05-2016, 09:49 AM
Replies: 1
Views: 3,179
Posted By KamilSJaron
Question visualisation of RNAseq (kallisto to IGV)

Hello everyone,

as others, I am quite excited about pseudo alignment produced by kallisto in minutes instead of real alignment computed for hours. Now, it would be useful to visualise it using...
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