User: darxsys

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darxsys190
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190
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Croatia
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5 years, 2 months ago
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Posts by darxsys

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Estimating RPKM or TPM in RNA-Seq data
... Yes, you're right. I read that in this paper too and forgot about it. What I wrote is an estimate of NPM and can easily be converted to TPM or TPM can be calculated from your formulas. I am also aware of TPM benefits and RPKM drawbacks, but as you said, it should not make a whole lot of difference f ...
written 5.6 years ago by darxsys190
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Comment: C: Count number of mapped raw reads for each transcript in SAM file
... I wrote an implementation in C++ for my purposes using seqan library to do just that. Works fairly fast. Didn't try it on such big files though. You can try doing something similar. With seqan, it should be relatively painless. ...
written 5.6 years ago by darxsys190
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Estimating RPKM or TPM in RNA-Seq data
...  I am trying to test a software for abundance estimation, and I am trying to think of a way to generate my own set of reads, but knowing the expected values of benchmark relative abundances in advance to make sure I can compare the output to the benchmark. If I have a set of N transcripts, and I gen ...
rpkm rna-seq written 5.6 years ago by darxsys190 • updated 5.6 years ago by Rob4.6k
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Comment: C: Getting transcript annotation in BED format along with reference seq.
... What I've noticed is that the simulator returns an error trying to convert field number 10 to exon length. I don't see any such corresponding field in this bed3 file. ...
written 5.6 years ago by darxsys190
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Comment: C: Getting transcript annotation in BED format along with reference seq.
... Probably, If I knew what fields correspond to which in these two file formats. I am not very familiar with variations between bed files. ...
written 5.6 years ago by darxsys190
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Comment: C: Getting transcript annotation in BED format along with reference seq.
... Unfortunately, it seems that a bed file produced by gff2bed is not how it should look like. I've compared bed fields from such files with those provided by the mentioned simulator's examples, and they differ quite a lot so I can't use the simulator on gff2bed files. This is how simulator expects th ...
written 5.6 years ago by darxsys190
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Getting transcript annotation in BED format along with reference seq.
... I want to test how different RNA transcript abundance software work. I would like to use this simulator to produce reads from transcripts because it enables to automatically generate transcript abundances. To do that, I have to provide transcript annotation file in BED format and a reference seque ...
genome annotation rna-seq transcriptome written 5.6 years ago by darxsys190 • updated 5.6 years ago by Alex Reynolds31k
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Comment: C: Paired-end reads - what is what?
... So in the second file, if it says: TTCAG, that actually corresponds to CTGAA in the forward strand? ...
written 5.6 years ago by darxsys190
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Paired-end reads - what is what?
... This is probably a dummy question, but I haven't found an explanation and I want to be sure. When paired-end sequencing is done, there are usually 2 fastq files generated, one with "left" mates and the other with "right" mates. Assuming that mates in the first file are read from the forward strand, ...
paired-end rna-seq sequencing written 5.6 years ago by darxsys190 • updated 5.6 years ago by thackl2.8k
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Comment: C: SAM format paired-end alignment handling
... Thank you. I am wondering what do you mean by the fact that only one of the reads can have multiple mappings? How does that look like? By multiple mappings, I was thinking of a case where the paired-end read (both mates concordantly) maps to different positions on the same transcript equally well, ...
written 5.7 years ago by darxsys190

Latest awards to darxsys

Supporter 5.6 years ago, voted at least 25 times.
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Pacbio Quiver Consensus - How To Use?
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Blast E Value Calculation

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