User: Corentin
Corentin • 300
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PhD student in Bioinformatics, with some experience in RNA-seq and de novo genome assembly.
Posts by Corentin
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... It depends on the language you want to use, but the principle is the same for every language:
You need to write a "for" loop that will read all the snp ids you want to process, and inside the loop you use the id to query the REST API.
There are plenty of tutorials about for loops available, you al ...
written 10 days ago by
Corentin • 300
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... You are welcome :) (by the way, I meant no offense in my post) ...
written 14 days ago by
Corentin • 300
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... For SNP-SNP interactions, all elements that are specific to a given SNP (rsID, risk allele, mapped gene, chromosome location etc) are separated by an "x" (eg "rs1336472-A x rs4715555-G")
From: https://www.ebi.ac.uk/gwas/docs/faq
Always try to check the documentations before asking a question ...
written 15 days ago by
Corentin • 300
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... One way to do it is ot use ensembl REST API: https://rest.ensembl.org/
You can fetch the variants in LD with your variant of interest: https://rest.ensembl.org/documentation/info/ld_id_get
and then intersect it with your list of knwon SNPs. It is then easy to set up a loop to process variants in ba ...
written 15 days ago by
Corentin • 300
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C: MaSuRCA, Flye assembly error
... Just to get this out of the way: are you using "~" instead of "/home/username/" in your full path ? Sometimes "~" is not correctly interpreted.
Also, try to read the file with *"cat -v mr.41.15.15.0.02.1.fa"*, and check if any **"^M"** characters appear (these are windows new line). ...
written 21 days ago by
Corentin • 300
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C: MaSuRCA, Flye assembly error
... Please check that your locale settings: LANG = "en_US.UTF-8" are supported and installed on your system.
It seems that your OS does not support "en_US.UTF-8". Try to set it up with:
LANG=C perl -e exit
You can also try to reconfigure your locales with "dpkg-reconfigure locales"
(source: ...
written 21 days ago by
Corentin • 300
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... I do not know about your specific project but in general contigs are from genome assemblies and transcripts are from transcriptome assemblies. These are two different things:
- In genome assembly your goal is to create a complete representation of the genome (Ideally with a fasta containing one sequ ...
written 21 days ago by
Corentin • 300
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... There is similar question here : https://www.biostars.org/p/359525/ ...
written 26 days ago by
Corentin • 300
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... It is impossible to say without knowing any details about the project. Why do you need to filter the sequences?
Even when knowing the details, there is probably no perfect threshold, it is often a trade-off between removing artifacts (I guess this is what you want to do) and not losing too much inf ...
written 26 days ago by
Corentin • 300
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C: How to append two fasta files?
... Apparently faidx is giving this error if the coordinates are reversed:
[faidx] Zero length sequence: ...
written 5 weeks ago by
Corentin • 300
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