User: yarmda

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yarmda0
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Posts by yarmda

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Comment: C: How to use ANNOVAR with bacterial genome?
... Hi Jen, When you say it creates a "database" what exactly do you mean? I started following the steps to produce a custom genome - I uploaded my ref genome and used the normalize fasta tool, but this just produces a slightly differently formatted fasta file. This may work, but then what do I include ...
written 12 months ago by yarmda0
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How to use ANNOVAR with bacterial genome?
... I am trying to automatically generate annotations for a VCF file generated from the Mtb H37Rv genome. ANNOVAR seems like a possible route to do this, but each of its scripts require a --buildver parameter which indicates the version of the genome in use. I have my VCF file and a file of Mtb genome ...
annovar variant annotation written 12 months ago by yarmda0 • updated 12 months ago by Jennifer Hillman Jackson25k
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FastQ to SAM conversion runs out of memory and fails
... I'm trying to use the NGS Picard FASTQ to SAM conversion tool to start an RNA-Seq analysis. I am transferring FASTQ files from the EBI database, which offers the option to submit a job to Galaxy to pick up the files. This worked, but the conversion to SAM fails because the process uses more memory t ...
picard rna-seq written 2.4 years ago by yarmda0 • updated 2.4 years ago by Jennifer Hillman Jackson25k

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