User: SaltedPork

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SaltedPork110
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Posts by SaltedPork

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Having trouble with Seqkit Replace, trying to rename fasta headers from file
... My fastas look like: >123456789.1 AGCT >123456789.2 AGCT >222221122.1 AGCT The fasta does not have end of line characters so the sequence is all on one line. The fasta headers have a .1 .2 .3 and so on up to .8 at the end of them. cat ids.txt 123456789 1 ...
seqkit written 7 months ago by SaltedPork110 • updated 8 weeks ago by Mark800
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Comment: C: GPU based parallel processing in genomics tools
... Depends on your situation. Workstation for us works better because we are completely in charge of it, not IT department. But rack mounted might get you better specs, and the noise/heat isn't in the office. ...
written 11 months ago by SaltedPork110
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Answer: A: SSD or HHD for genome analisys
... If this is for a Desktop/Workstation then I would install your OS and pipelines on an SSD. Once an analysis is complete, move the data onto HDDs for backup. ...
written 11 months ago by SaltedPork110
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Comment: C: Rename fasta headers from CSV
... Thanks, but my headers don't have the second value in them, just the _AA. Any ideas? I've tried playing with the regex but no luck. ...
written 16 months ago by SaltedPork110
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Comment: C: Rename fasta headers from CSV
... Thanks, no they don't. ...
written 16 months ago by SaltedPork110
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Comment: C: Rename fasta headers from CSV
... Thanks for this answer, very clear. I am getting fasta headers like >_AA, >_BB. The bit from the CSV is not there. Could you explain what the sed and regex bits are doing. Sed is replacing commas with tabs in the csv, is this because seqkit doesn't handle the commas? Also what is the _ doing ...
written 16 months ago by SaltedPork110
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Rename fasta headers from CSV
... I have a CSV file that looks like this: 201200175,A/name1/175/2012 201200287,A/name2/287/2012 201200845,A/name3/845/2012 Currently my fasta headers look like: >201200175_AA >201200175_AB >201200175_BB and I want to change it to: >A/name1/175/201 ...
perl python bash written 16 months ago by SaltedPork110 • updated 16 months ago by SMK1.9k
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Rename FASTA headers based on filename
... Hi FASTA header looks like: >1570-13.segment.flu1_PB2 >1570-13.segment.flu2_PB1 >1570-13.segment.flu3_PA etc Filenames looks like: 201301234.fasta I want to have FASTA headers that looks like: >201301234_PB2 >201301234_PB1 >201301234_PA I have ...
bash written 16 months ago by SaltedPork110 • updated 16 months ago by SMK1.9k
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Comment: A: Benchmarking GPUs with ONT Guppy 3.0
... https://www.youtube.com/watch?v=2JmWrO2bcsQ Here's a benchmark video comparing Titan RTX and Quadro cards. Haven't used GUPPY, but I would imagine the Titan RTX is much better value for money. ...
written 16 months ago by SaltedPork110
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Answer: A: Testing Illumina reads for contamination
... Can't help with Python bins. We have viral reads and filter out any human contamination. This is done by mapping the reads to an indexed file with both human reference genome and a viral database. Any read that maps to human gets discarded. Any read that maps to viral gets kept. ...
written 16 months ago by SaltedPork110

Latest awards to SaltedPork

Great Question 9 months ago, created a question with more than 5,000 views. For Using BWA Index and i get 5 output files, but BWA-mem asks for just 1
Popular Question 9 months ago, created a question with more than 1,000 views. For How can I use Samtools to map coverage distribution?
Popular Question 10 months ago, created a question with more than 1,000 views. For Any ideas on converting IUPAC ambiguity codes in a fasta file
Popular Question 15 months ago, created a question with more than 1,000 views. For How can I use Samtools to map coverage distribution?
Popular Question 18 months ago, created a question with more than 1,000 views. For How can I use Samtools to map coverage distribution?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How can I use Samtools to map coverage distribution?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Getting a bash pipeline to output non-zero exit code when a step fails
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Using BWA Index and i get 5 output files, but BWA-mem asks for just 1
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Supporter 2.8 years ago, voted at least 25 times.
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Using BWA Index and i get 5 output files, but BWA-mem asks for just 1

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