User: c_dampier

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c_dampier60
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Posts by c_dampier

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Appropriate bed files from library capture kit for computing on target coverage
... I'm not sure how typical this situation is, where the Covered and Regions files are exactly the same intervals. In case it is not the norm, I am supplementing the response from [finswimmer][1] with a couple old posts for reference. I use this prior post for reference on what the different Agilent b ...
written 8 weeks ago by c_dampier60
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Comment: C: Can Salmon's quantification method accommodate concatenated reads of varying len
... Thank you, [ATpoint][1]. Your comments are helpful, as is the link to the very informative discussion on read pairs with different lengths. I regret not finding it when I initially started searching for questions related to mine. Thank you for the link. [1]: https://www.biostars.org/u/25721/ ...
written 8 months ago by c_dampier60
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Comment: C: awk or/and cut command for reformatting sequence header identifiers of fastq fil
... You're welcome, qinglong. I apologize for potentially leading you astray with my original code. Glad h.mon was there to save us. ...
written 8 months ago by c_dampier60
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Comment: C: awk or/and cut command for reformatting sequence header identifiers of fastq fil
... Thank you, [h.mon][1]. I think the edited code will be safer. [1]: https://www.biostars.org/u/6093/ ...
written 8 months ago by c_dampier60
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Answer: A: awk or/and cut command for reformatting sequence header identifiers of fastq fil
... I think this (edited per h.mon comments) awk code will give you the desired output: awk 'NR%4==1 {$3=""} NR%4==3 {$0=substr($0,1,1)} {print $0}' The first rule finds each 4th line starting with line 1, and its associated action changes the third field (separated by " ") to empty. The next ru ...
written 8 months ago by c_dampier60
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Can Salmon's quantification method accommodate concatenated reads of varying length (from independent sequencers) in a single fastq file?
... Good evening My question is whether it is more appropriate to feed Salmon a single concatenated fastq file or multiple sequencer- and read-length-specific fastq files when the reads in the fastq file (or files) have been generated at different times with different sequencing lengths for a given sam ...
salmon rna-seq sequencing written 8 months ago by c_dampier60

Latest awards to c_dampier

Scholar 8 months ago, created an answer that has been accepted. For A: awk or/and cut command for reformatting sequence header identifiers of fastq fil
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: awk or/and cut command for reformatting sequence header identifiers of fastq fil

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