User: susan.klein

gravatar for susan.klein
susan.klein50
Reputation:
50
Status:
New User
Location:
Oceania
Last seen:
2 years, 5 months ago
Joined:
4 years, 10 months ago
Email:
t***********@csiro.au

Posts by susan.klein

<prev • 27 results • page 1 of 3 • next >
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Answer: A: magicblast errors using SRA
... ah I worked it out - they are protected SRAs.. so if you are scripting against their full list of experiments, you have to filter them out.. or ignore the errors. Annoyingly the read data is deemed to contain individual person data so there's no way to get around it. :( ...
written 2.5 years ago by susan.klein50
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magicblast errors using SRA
... Hi, anyone using magicblast to search SRAs ? I find that some SRAs work while others give errors like below. Also anyone know who to ask?? Thanks, S. searching SRR4484512 VDB: 2016-11-03T02:53:40 . err: query unauthorized while resolving tree within virtual file system module - failed to resolve ...
blast written 2.5 years ago by susan.klein50
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Comment: C: BLAST options error: tried to set option (130) and value (1), line (537)
... I think this is actually because it was pointing to an incorrect database. ...
written 3.3 years ago by susan.klein50
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Answer: A: BLAST options error: tried to set option (130) and value (1), line (537)
... Hi, was this ever solved? I'm getting same error on a protein search: blastp -remote -query 1.faa -db nr -out out.blast -outfmt '6 qseqid sseqid pident length slen qstart qend sstart send evalue bitscore stitle' -evalue 1e-10 -max_hsps 1 BLAST options error: err:tried to set option (130) and value ...
written 3.3 years ago by susan.klein50
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Maf or hal alignment format conversion
... Hi,   I am using progressiveCactus https://github.com/glennhickey/progressiveCactus and I want to view the alignments and extract a consensus sequence. I don't want to use the UCSC genome browser. Does anyone know how to convert from hal or maf format (the only two that can be output or converted ...
alignment written 3.3 years ago by susan.klein50
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Comment: C: Bulding a pangenome consensus from many individuals
... Hi,   the problem is not a classical pangenome one like you describe. I have already done that with no problems. I want to be able to make a pseudo-genome that contains all large indel variants. I hoped I could do this by aligning and obtaining the consensus with something like cactus but I now se ...
written 3.3 years ago by susan.klein50
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Bulding a pangenome consensus from many individuals
... Hi, I need to make a pangenome as a reference to compare 15 closely related bacterial strains. I have 15 assemblies with 20-30 contigs each. I can easily compare all of them to a single reference using any number of programs but unless the reference contains all the mobile element variants and phag ...
genome alignment written 3.3 years ago by susan.klein50 • updated 3.2 years ago by Cyril Frantzen0
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Comment: C: Variant Calling With Bcftools Call
... Hi,   has this been resolved. I have done fresh installs of samtools and bcftools and get: [vcf.c:753 bcf_hdr_read] invalid BCF2 magic string: only BCFv2.2 is supported Its very frustrating. Also I cannot use GATK, I can't get Java 1.7 on my Debian system (yet) and it always gives me numerous ja ...
written 4.5 years ago by susan.klein50
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Comment: C: Extract coverage per feature from a bam and bed to a file
... Yes! Thanks very much, that worked. ...
written 4.7 years ago by susan.klein50
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Comment: C: Extract coverage per feature from a bam and bed to a file
... This sounds very plausible, and one of those magic secrets you just never know, unless you went to Hogwarts.. thanks Sean, I'll give it a go. ...
written 4.7 years ago by susan.klein50

Latest awards to susan.klein

Popular Question 3.0 years ago, created a question with more than 1,000 views. For Genbank to bed conversion for bedtools analysis
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Genbank to bed conversion for bedtools analysis
Popular Question 3.2 years ago, created a question with more than 1,000 views. For BioPython SeqRecord attributes
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Extract coverage per feature from a bam and bed to a file

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