User: tim.booth

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tim.booth20
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Posts by tim.booth

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Concatenate fastq files before or after trimming?
... Aside from the issue noted by @Asaf, the only other consideration is if you want overall trimming statistics then you will have to numerically add up the numbers from all the TrimGalore log files. But most people don't worry too much about these. You say you want to concatenate before aligning but ...
written 6 months ago by tim.booth20
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Comment: C: How to calculate GC% at 1st, 2nd and 3rd codon position for each sequence in a m
... Not really an answer but the reason your command is slow is that it launches and terminates both `grep` and `sed` for every single line of the .fasta file. In `sed` you can add a regex to switch on the replacement, so: `sed '/^>/!s/\(..\)./\1/g' cds.fasta` Where `/^>/!` means match all lines ...
written 6 months ago by tim.booth20
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Alignment Score (AS) tag in minimap2
... Hi, I'm working with some SAM files generated by minimap2. The reads have been aligned to a spike-in reference so I'd like to use the alignment scores from the BAM file to get an estimate of the raw error rate introduced during sequencing. My understanding was that the maximum alignment score (AS) ...
minimap2 alignment sam written 6 months ago by tim.booth20
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Answer: A: Compare specific parts of two columns in a text file in Linux
... Hi, The last answer from @cpad0112 looks right to me, in that it directly answers your question and extracts and compares n1 and n2 from the third and fourth columns. However I note that the example file looks rather like a simplified version of SAM data, and you did ask for alternative approaches ...
written 6 months ago by tim.booth20

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