User: glihm

gravatar for glihm
glihm560
Reputation:
560
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Trusted
Location:
France
Last seen:
5 months, 4 weeks ago
Joined:
3 years, 1 month ago
Email:
p******@me.com

Hey there!

I you are looking for help or someone to talk about one of the following categories:

**Programming**: C, C++, Python

**Bioinformatics**: RIBO-seq (since 2015), RNA-seq (since 2015), 16S metagenomics with USEARCH (since 2014)

 

Please feel free to contact me at bertinp17@gmail.com and let's have a talk! :)

Posts by glihm

<prev • 110 results • page 1 of 11 • next >
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Answer: A: removing a part of sequence of all genes
... Hello Sara, you can use [cutadapt][1] to remove adapters (poly-A included). As the poly-A is usually found at the 3' end of reads, you can use the following as suggested by cutadapt documentation: `cutadapt -a "A{100}" -o output.fastq input.fastq` [1]: http://cutadapt.readthedocs.io/en/stable/ ...
written 11 months ago by glihm560
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Comment: C: transcript and fasta sequence
... Your request is now clearer. The answer of @genomax is in this case well suited for your issue by using assembly merging. ...
written 11 months ago by glihm560
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Comment: C: merging table columns
... Pierre, you're faster than me! :p ...
written 11 months ago by glihm560
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Answer: A: transcript and fasta sequence
... Hello qudrat, 1. If you are interested in IDENTICAL sequences, you can simply write a very short script to extract identical sequences in both files. 2. You want to apply a "**similarity**" score, if so I strongly suggest using multi-aligners (BLAST or MUSCLE for instance) and then parse the resu ...
written 11 months ago by glihm560
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Comment: C: formatting problem (awk/bash)
... Real data are always better as some special cases must be handled depending on your expression values and ID. ;) **edit**: Do you always have r1 lines, and then r2 lines and so on? Or it can be unordered? ...
written 11 months ago by glihm560
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Comment: C: How can I replace pathway names with gene names?
... Hello fp89, you can try using `code formating` to display some data-structures. It will be easier to understand your request. An other point that might help you posting your questions, you can first giving the actual state of the files, and then, the desired state. Like this, people can take your fe ...
written 11 months ago by glihm560
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Comment: C: RPKM documentation is needed!
... Can you give us the header of your file for instance? :) The definition of RPKM can be found [here][1] and [here][2] to give you several ways to explain it. And to give you one of the important point of these links, __"RPKM is a unit of expression, not a method"__. [1]: http://www.rna-seqblog.c ...
written 11 months ago by glihm560
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Comment: C: warning message after Deseq2
... Hello BioDH, Can you confirm that you are working with **Pair-end** data? This warning is telling that for 3752 reads of your BAM file, one of the two reads of the pair if missing. You should consider checking the program that gives you the BAM file. Or, you can skip this warning if you think that ...
written 11 months ago by glihm560
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Answer: A: how to remove Overrepresented sequences for paired end with cutadapt?
... Hello Lila M, as mentioned in the [cutadapt documentation][1] you are doing the things well. You can use several adapters (-a/g multiple time) and you can set the adapter search for a particular mate of the pair (-a/g for R1 and -A/G for R2). So, if you try the command you mentioned it should wor ...
written 11 months ago by glihm560
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Comment: C: Sam FLAGS : how could a read be described as "read unmapped" but "read in revers
... Actually, I don't think you've to care about unmapped reads in general. Except that if the unmapped reads are your reads of interest (filtering data for instance). > practically they are the same because they are unmapped anyway? Exactly. ;) The only thing you have to keep in mind is that, for ...
written 11 months ago by glihm560

Latest awards to glihm

Scholar 11 months ago, created an answer that has been accepted. For A: sequence alignment vs mapping
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Why not Windows
Centurion 11 months ago, created 100 posts.
Supporter 11 months ago, voted at least 25 times.
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 23 months ago, created an answer that has been accepted. For A: sequence alignment vs mapping
Scholar 24 months ago, created an answer that has been accepted. For A: sequence alignment vs mapping
Appreciated 24 months ago, created a post with more than 5 votes. For A: How can I separate a FASTA file into multiple exon and CDS files?
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: How can I separate a FASTA file into multiple exon and CDS files?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Why not Windows
Scholar 2.4 years ago, created an answer that has been accepted. For A: sequence alignment vs mapping
Rising Star 2.9 years ago, created 50 posts within first three months of joining.
Scholar 3.0 years ago, created an answer that has been accepted. For A: sequence alignment vs mapping
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Why not Windows
Scholar 3.0 years ago, created an answer that has been accepted. For A: sequence alignment vs mapping
Scholar 3.0 years ago, created an answer that has been accepted. For A: sequence alignment vs mapping

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