User: williamsbrian5064

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Posts by williamsbrian5064

<prev • 153 results • page 1 of 16 • next >
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Computing all possible single amino acid substitutions for a protein
... Hi, I am working on a project with a particular protein of interest. I was wondering if anyone knew of any software that can take a protein and generate a file that shows all the possible amino acid substitution for that protein? I saw that provean has done this with humans [here][1] (provean scor ...
genome gene written 19 days ago by williamsbrian5064170
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Plink formatting issues map file has zeros for chromosome and physical position
... Hi, I have a vcf file that I am converted into ped and map files for plink. When I look at the map file that plink creates, it has zeros for chromosome and physical position. I can seem to figure out why or any documentation on plinks website. This is what I am running plink --vcf test.vcf --r ...
software error assembly genome written 5 weeks ago by williamsbrian5064170
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Comment: C: Software for inversions in short read WGS
... Yeah... the more I think about it makes me think there is just poor coverage here :( ...
written 6 weeks ago by williamsbrian5064170
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Comment: C: Software for inversions in short read WGS
... I didn't do WGS on any controls. This sample is a horse and we don't very much horse related project so I didn't want to spend the money to sequence a control. I figured if I could something I could do sanger sequence to confirm. This was my thought process, and this could be incorrect since it is ...
written 6 weeks ago by williamsbrian5064170
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Software for inversions in short read WGS
... Hi, I apologize in advance for the vague titled. I did some WGS on a sample that had an interesting disease. The disease is X-linked and the sample was taken from a male. There have been a couple of papers published about this disease and they found a large inversion ~3kb in an intron. I was lookin ...
software assembly next-gen alignment written 6 weeks ago by williamsbrian5064170 • updated 6 weeks ago by WouterDeCoster39k
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Comment: C: BWA mem skip orientation
... Thank you two so much for sticking through this with me! I really appreciate the BioStar community. ...
written 7 weeks ago by williamsbrian5064170
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Comment: C: BWA mem skip orientation
... I figured it out. I shamefully aligned R2 twice (see below). This is most dishonorable ...
written 7 weeks ago by williamsbrian5064170
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Comment: C: BWA mem skip orientation
... *Sigh* ....I am embarrassed to say that when running `bwa mem` I put in R2 in twice so this all makes sense bwa mem -M -t 16 -R '@RG\tID:H02396_S47_0001\tSM:H02396\tPL:illumina\tLB:H02396_lib1\tPU:barcode_H02396' Equus_caballus.EquCab3.0.dna_sm.toplevel.fa H02396_S47_R2_001_trim_paired.fastq.g ...
written 7 weeks ago by williamsbrian5064170
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Comment: C: BWA mem skip orientation
... I am just curious what the actual issue is. The trimming seems fine, bwa seems to be fine, the bam file seems to be fine? I could see snps and what not. Maybe there is an issue with bcftools? I uses samstools flagstat and that worked. Any suggestions on where to look next? ...
written 7 weeks ago by williamsbrian5064170
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Comment: C: BWA mem skip orientation
... It is my data but it was stored on our labs AWS account. There was a new reference sequence for this species so I just wanted to align the reads to the new reference. Maybe there was an issue with the AWS download? ...
written 7 weeks ago by williamsbrian5064170

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