User: erwan.scaon

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erwan.scaon550
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Location:
Limoges - CBRS - France
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http://www.unilim.fr/r...
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2 days, 10 hours ago
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Posts by erwan.scaon

<prev • 74 results • page 1 of 8 • next >
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Answer: A: Fasta file filtering
... You can easily achieve this with [seqtk][1]. Quoting from the manual : > Extract sequences with names in file name.lst, one sequence name per line: > seqtk subseq in.fq/fa name.lst > out.fq/fa [1]: https://github.com/lh3/seqtk ...
written 6 weeks ago by erwan.scaon550
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Comment: C: Parsing Blast output on linux/unix
... If you don't have to stick to XML, you should try tabular output (outfmt 6). Then you can start learning how to parse it from [ncbi webinar][1]. Basic UNIX command lines will work far better on tabular output compared to XML. [1]: https://www.youtube.com/watch?v=BIBL-wYhAl4 ...
written 6 weeks ago by erwan.scaon550
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Comment: C: Kallisto TPM values
... You should post or link your question on the [google_group][1]. You may also find an answer to your question from previous posts on this google_group. Does [this one][2] help ? [1]: https://groups.google.com/forum/#!forum/kallisto-sleuth-users [2]: https://groups.google.com/forum/#!searchin/k ...
written 6 weeks ago by erwan.scaon550
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Comment: C: Search only plasmids from NT database using local BLAST
... *Ps* : If you are not using blast+ 2.8.0 & BLAST v5 databases (as mentionned in my link), you can still use the "-seqidlist" parameter from previous versions of blast+ : > -seqidlist > Restrict search of database to list of SeqId's With the "list of SeqId's" being all plasmids SeqId's ...
written 6 weeks ago by erwan.scaon550
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Comment: C: Search only plasmids from NT database using local BLAST
... You should have a look [here][1]. [1]: https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf ...
written 6 weeks ago by erwan.scaon550
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Comment: C: Identifying CNVs from targeted amplicon sequencing
... Maybe you could have a look at COV'COP : [git][1], [publication][2]. [1]: https://git.unilim.fr/merilp02/CovCop [2]: https://academic.oup.com/bioinformatics/article/33/10/1586/2962858 ...
written 7 weeks ago by erwan.scaon550
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Comment: C: Kallisto TPM values
... I did check some "abundance.tsv" files from many Kallisto runs in many projects. The "tpm" column always sum up to 1 million. Did you double check ? Which Kallisto version are you using ? I did check with v0.43.0 & v0.44.0. ...
written 7 weeks ago by erwan.scaon550
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Comment: C: Please suggest your idea for variant calling analysis of many BAM files from who
... Are you looking for germline or somatic variants ? If you end up using GATK, regarding your focus on specific genes, you can use an [interval_list][1] to restrict the search (and save time). [1]: https://gatkforums.broadinstitute.org/gatk/discussion/1319/collected-faqs-about-interval-lists ...
written 11 weeks ago by erwan.scaon550
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Comment: A: STAR options for RNA Seq
... You should refer (if not already done) to 3.2.2 in STAR manual : "ENCODE options" (for long RNA-Seq pipeline). If you want to read more about the latest ENCODE options for RNA-Seq, you will find documentation [here][1]. [1]: https://github.com/ENCODE-DCC/long-rna-seq-pipeline/releases/tag/v2.3. ...
written 11 weeks ago by erwan.scaon550
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Comment: C: How to make a custom gtf or gff3 file with a list containing transcript loci
... Maybe this [post][1] can help (in OP comments, there are hints about how to create a custom GTF). [1]: https://www.biostars.org/p/306859/ ...
written 11 weeks ago by erwan.scaon550

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
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Scholar 3 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
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Scholar 6 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
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