User: Picasa
Picasa • 380
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Posts by Picasa
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C: What is an optical map ?
... Thanks for your link.
1 ) So can we say that Bionano optical map tend to replace Long reads sequencing (Pacbio and nanopore) ?.
2) I am not sure to understand what is the output of Bionano: raw reads ? if yes, what is the error rate ? ...
written 11 hours ago by
Picasa • 380
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... Hello everybody.
After several research I still don't understand what is an optical map.
1) This figure confuse me because it looks like the output of the optical map are sequences ?
https://upload.wikimedia.org/wikipedia/commons/thumb/e/e1/Optical_mapping.jpg/1000px-Optical_mapping.jpg
2) And ...
written 14 hours ago by
Picasa • 380
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... Dear Biostar,
Do you have the same kind of figures but after mapping with long reads like PacBio ? (I am looking for inversions)
https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
Thanks a lot. ...
written 5 weeks ago by
Picasa • 380
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... for option A, do you have a link to the pre-build blastb ?
because I have tried 2 methods :
makeblastb from nr.gz directly
and
update_blastdb.pl --decompress nr
and still got the
> [ERRO] field (2) out of range (1) in file: - ...
written 5 weeks ago by
Picasa • 380
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... Thanks I will try.
1) For the option A: How do you create your database (nr) and how much time is very slow ?
Because I got this error:
[ERRO] field (2) out of range (1) in file: -
2) I am not sure to understand the option B, because you mentioned "buggy", but the makeblastdb is working ? ...
written 5 weeks ago by
Picasa • 380
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... yes so apparently, some sequences don't start with '>' ...
written 5 weeks ago by
Picasa • 380
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... Ok.
Anyway. I have tried to make a database with this new fasta, with this command:
makeblastdb -in ../nr.arthropods.fasta -parse_seqids -dbtype prot -out nr.arthropods
and I got this error:
Building a new DB, current time: 09/10/2018 21:29:34
New DB name: db_blast/nr.arthropods
...
written 5 weeks ago by
Picasa • 380
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... done.
But I still got low number of sequence compared to the accession number:
grep '>' nr.arthropods.seqkit2.fasta -c
4133470
is it normal ? ...
written 5 weeks ago by
Picasa • 380
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... Hi,
I have done a SNPs analysis and now I have a VCF.
I would like to filter it but I don't know what is usually done. For instance I know that I can filter by:
- Remove samples that have > x% missing data
- Remove SNPs that have > x% missing data
- Remove SNPs with >x% MAF
Do you h ...
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... Using Arthropods: 6656 ...
written 5 weeks ago by
Picasa • 380
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