User: williamsbrian5064

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Posts by williamsbrian5064

<prev • 79 results • page 1 of 8 • next >
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Comment: C: Samtools mpileup taking a long time to finish
... Oh our lovely cluster admin. He is always so much fun to talk to :/ I will talk to him and see what he says. I think it will cause an issue. I guess I could just try just submitting jobs by chromosome? Maybe take a bit but none is really using our cluster since it's the summer here. Then just comb ...
written 5 days ago by williamsbrian506460
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Comment: C: Samtools mpileup taking a long time to finish
... It is a high-performance compute cluster ...
written 5 days ago by williamsbrian506460
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Comment: C: Samtools mpileup taking a long time to finish
... You can run samtools on each chromosome all at once? This wont give you any issues? GNU parallel doesn't seem to bad. Seems like a valid option. ...
written 5 days ago by williamsbrian506460
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Samtools mpileup taking a long time to finish
... Hi, I am using samtools for variant calling. The issue I am having is that samtools mpileup seems to be taking a very long time. I am running samtools on a cluster and have a set how long samtool will run. The first time I tried this I gave it 7 days to run with 256 Gbs of RAM. The resulting file o ...
genome assembly sequence alignment written 5 days ago by williamsbrian506460 • updated 5 days ago by ATpoint4.4k
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Comment: C: Issues with Illumina Universal Adapters
... I was really referring to some of the flag it will call when looking at RNA seq data. Not saying it can't do RNA-seq data ...
written 11 days ago by williamsbrian506460
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Issues with Illumina Universal Adapters
... Hi, I am attempting to trim some RNA-Seq data. I am having some issues with Illumina universal adapters. I am using trimmomatic to trim the reads and I used trimmomatics TruSeq3-PE.fa file to help trim the adaptors, but there still seems to be a lot of the Illumina universal adapters left. Is this ...
next-gen rna-seq sequencing written 11 days ago by williamsbrian506460 • updated 11 days ago by genomax49k
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Comment: C: Issues with Variant Calling from old bam files
... Wooooooooooow. The problem came up when I did that pointless trimming. I made an error and trimmed R1 twice instead of R1 and R2. Thanks for the help everyone. I really really appreciate your help. ...
written 12 days ago by williamsbrian506460
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Comment: C: Issues with Variant Calling from old bam files
... 551741879 + 0 in total (QC-passed reads + QC-failed reads) 2724021 + 0 secondary 0 + 0 supplementary 59155766 + 0 duplicates 549580515 + 0 mapped (99.61% : N/A) 549017858 + 0 paired in sequencing 274508929 + 0 read1 274508929 + 0 read2 0 + 0 properly paired (0.00% ...
written 12 days ago by williamsbrian506460
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Comment: C: Issues with Variant Calling from old bam files
... hmm.. how do you do that? ...
written 12 days ago by williamsbrian506460
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Issues with Variant Calling from old bam files
... Hi, I am in the process of realigning some samples to an updated genome. For the majority of the samples, I had the original fastq files. For a couple of my samples, I was only given a bam file. So what I did was use Picards "SamToFastq" function to convert the bam file back to a fastq file. Since ...
genome assembly next-gen alignment written 12 days ago by williamsbrian506460

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