User: david.4.ray

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david.4.ray10
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United States
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3 years ago
Joined:
3 years, 6 months ago
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d**********@gmail.com

Posts by david.4.ray

<prev • 6 results • page 1 of 1 • next >
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Comment: A: [bcf_sync] incorrect number of fields (0 != 5) at 0:0
... Update: I ran `head` and `tail` on my .vcf file and it doesn't look so good after all. head yields what you would expect. Standard headers and such. tail does something very strange. In fact, it appears to be trying to read a binary rather than a text file. No idea where this development is arisi ...
written 3.1 years ago by david.4.ray10 • updated 6 months ago by RamRS20k
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[bcf_sync] incorrect number of fields (0 != 5) at 0:0
... I am attempting to call variants on some genomes and troubleshooting an error I'm getting from bcftools. My commands are as follows: $SAMTOOLS_HOME/samtools mpileup -Q30 -C50 \ -uf $REF_HOME/$REFGENOME$INPUT/$SPECIES"_R3_noDup.bam" \ >$SPECIES"_mPileUp.vcf" Followed by: ...
software error genome samtools snp bcftools written 3.1 years ago by david.4.ray10 • updated 17 days ago by zx87546.8k
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Comment: C: BWA MEM indexing
... Yep.  That was it.  Working just fine now. ...
written 3.5 years ago by david.4.ray10
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Comment: C: BWA MEM indexing
... No.  I have actually performed a full reference-based assembly of the genome using these reads.  I'll explain.   We have a working pipeline that will index the reference genome, then process the raw reads from the genome we want to assemble using that reference.  One of the processing steps is to u ...
written 3.5 years ago by david.4.ray10
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Comment: C: BWA MEM indexing
... Yeah, I was afraid it might be something less simple.  It's interesting, though, because I previously successfully assembled the genome using bwa aln and exactly the same files that I'm using here.  The only difference is that I've switched to bwa mem.  Does that change your response at all? ...
written 3.5 years ago by david.4.ray10
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BWA MEM indexing
... I'm a relative newbie and trying t work my way through using bwa mem.  I've successfully aligned PE reads to a reference genome previously using bwa aln but I thought this might work better. I'm getting the following output: [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, ...
assembly alignment written 3.5 years ago by david.4.ray10 • updated 3.5 years ago by Istvan Albert ♦♦ 79k

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