User: Picasa

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Picasa380
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Posts by Picasa

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Comment: 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 Picasa380
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What is an optical map ?
... 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 ...
assembly scaffold optical map written 14 hours ago by Picasa380
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Pacbio inversion visualization and IGV
... 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. ...
inversion igv written 5 weeks ago by Picasa380
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Comment: C: Custom nr database with only arthropods ?
... 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 Picasa380
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Comment: C: Custom nr database with only arthropods ?
... 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 Picasa380
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Comment: C: Custom nr database with only arthropods ?
... yes so apparently, some sequences don't start with '>' ...
written 5 weeks ago by Picasa380
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Comment: C: Custom nr database with only arthropods ?
... 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 Picasa380
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Comment: C: Custom nr database with only arthropods ?
... 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 Picasa380
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Parameter to filter a VCF of SNPs?
... 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 ...
vcf parameters snp written 5 weeks ago by Picasa380 • updated 5 weeks ago by RamRS18k
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Comment: C: Custom nr database with only arthropods ?
... Using Arthropods: 6656 ...
written 5 weeks ago by Picasa380

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