User: Bastien Hervé

gravatar for Bastien Hervé
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170
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Location:
Limoges, CBRS, France
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7 hours ago
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1 year ago
Email:
b****************@orange.fr

Posts by Bastien Hervé

<prev • 30 results • page 1 of 3 • next >
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Comment: C: STAR index fail with gtf, works with gff3
... Well played, works better now. I didn't think this option could interfer... If you want to add this as an answer, I'll mark it as accepted. Thank you ...
written 14 hours ago by Bastien Hervé170
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STAR index fail with gtf, works with gff3
... I try to create an index with STAR version STAR-2.5.2b, I got an error at the "processing annotations GTF" step with a GTF file, so I try with the associate GFF3 and it's working, question is, why ? I know, I could use that GFF3 file but I don't want to introduce an other file in my RNA-seq workflow ...
gff3 gtf star written 1 day ago by Bastien Hervé170
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Answer: A: parsing vcf file
... import sys import re def parse_vcf(vcf_file): ###Open your file with open(vcf_file, 'r') as vcf_f: for line in vcf_f: ###Skip metadata lines if line[0] != '#': ###Split the line by "tab" to keep info fie ...
written 1 day ago by Bastien Hervé170
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Comment: C: Replacing the Chr names and position notions in vcf
... The way I think is a little bit different. I personally needed to rely on some code to understand how it works and how to do my own solution. In that way, I let OP some comments on key lines. Moreover, if OP just want a solution without getting involved in bioinformatics concept, here is one. Depend ...
written 3 days ago by Bastien Hervé170
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Comment: C: Replacing the Chr names and position notions in vcf
... I found it, it works well for me now. Note that, it is easier to find an error by providing the error message and the line involved. As Ram said, if you want to go deeper in file manipulation, you have to try coding by your own. Thereby, I let you some comments in the code '###' to have a better und ...
written 3 days ago by Bastien Hervé170
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Comment: C: Replacing the Chr names and position notions in vcf
... Right, i'll add it ! Thanks ...
written 6 days ago by Bastien Hervé170
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Answer: A: Replacing the Chr names and position notions in vcf
... As said above bcftools will be the best way to do it. If you want a code version here is mine Assuming that you have a match_table.txt file like this (separate by tab) : gi|996703411|ref|NW_015379183.1| chr1 gi|996703411|ref|NW_015379184.1| chr2 gi|996703411|ref|NW_015379185.1| chr3 gi|99670341 ...
written 6 days ago by Bastien Hervé170
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Answer: A: STAR analysis and alignment
... Actually typing : "star alignment requirements" on google give you what you need Then just Ctrl+F on publications using "require" key word https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/ >STAR’s high mapping speed is traded off against RAM usage: STAR requires ∼27 GB of RAM for aligning t ...
written 14 days ago by Bastien Hervé170
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Comment: C: STAR analysis and alignment
... That is a bit low for a human genome mapping according to this post (https://github.com/alexdobin/STAR) > 30GB of RAM for human genome And around 27GB of RAM for human genome on this STAR publication (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/) > STAR’s high mapping speed is trad ...
written 14 days ago by Bastien Hervé170
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Comment: C: fastq parsing inefficiencies with python
... I bet there is a faster way somewhere, like said above, taking advantage of ordering... If you have time maybe try in C language. And also if you really want to improve the calculation speed, try to catch which operation takes the longest time to process. I don't think the header_array filling will ...
written 15 days ago by Bastien Hervé170

Latest awards to Bastien Hervé

Scholar 1 day ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Scholar 16 days ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Supporter 28 days ago, voted at least 25 times.

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