User: andrew.phipps.00

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Posts by andrew.phipps.00

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Comment: C: Picard MarkDuplicates /SAM validation error
... Thanks a heap Pierre! ...
written 11 weeks ago by andrew.phipps.000
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Comment: C: Sort/Index bam prior to peak-calling ChIP-seq & deeptools bigwig visualisation
... Thanks for the suggestion! I hadn't thought of that (would have saved me a heap of time...) - I am going to try a few different alignment and peak calling tools, so will keep this in mind for the future! Cheers! ...
written 3 months ago by andrew.phipps.000
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Comment: C: Bowtie2-output to file
... Hi Satyajeet, I was able to get it working! The command above worked, and saved log files per sample. The main issue I had was with encoding between linux and microsoft (\r). The met file was a just in-case we needed - It was a first instance of running on a new cluster, so if there were performa ...
written 3 months ago by andrew.phipps.000
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Sort/Index bam prior to peak-calling ChIP-seq & deeptools bigwig visualisation
... Hi biostars community, First off I am quite new to NGS data analysis, and I am trying to find out answers for a few questions. I have gotten ChIP-seq data from a time-course and disease experiment, that I have trimmed and aligned with bowtie2, giving me .sam files, which I am converting to .bam ...
alignment chip-seq written 3 months ago by andrew.phipps.000
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Comment: C: Bowtie2-output to file
... Hi Satyajeet I am trying to get this log to work for batch processing multiple files - would something like this work? ``` #!/bin/bash #Alignment using bowtie2 for file in *.fq ; do (bowtie2 -p60 --met-file "path/to/metrics/$file_metrics.txt" -x path/to/refgenome -U "$file" -S "path/to/outp ...
written 3 months ago by andrew.phipps.000
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Comment: C: Running a large number of fastq files through FastQC and other downstream analys
... Thanks for that clarification! Saved me a heap of time. ...
written 3 months ago by andrew.phipps.000

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