User: SaltedPork

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SaltedPork100
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Posts by SaltedPork

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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 7 weeks ago by SaltedPork100
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Comment: C: Rename fasta headers from CSV
... Thanks, no they don't. ...
written 7 weeks ago by SaltedPork100
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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 7 weeks ago by SaltedPork100
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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 8 weeks ago by SaltedPork100 • updated 7 weeks ago by SMK1.8k
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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 8 weeks ago by SaltedPork100 • updated 7 weeks ago by SMK1.8k
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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 8 weeks ago by SaltedPork100
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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 8 weeks ago by SaltedPork100
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Answer: A: How to trim both pair end reads and remove low quality reads
... I use Trimmomatic frequently, it's pretty easy to use. Look at the manual, the default options are a good place to start example command: java -jar /home/folder.../Trimmomatic-0.38/trimmomatic-0.38.jar PE -threads 4 $Reads1 $Reads2 $sample.hq.1.fastq $sample.unpaired.1.fastq $sample.hq.2.fast ...
written 3 months ago by SaltedPork100
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Answer: A: How do you use BLAST?
... I use Blast mainly to aid in typing viral sequences. This info is then copied into a spreadsheet, and there is no filtering involved usually. ...
written 14 months ago by SaltedPork100
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Comment: C: How to get list of different bases and their positions from an alignment?
... they are about 92% similar, ~700 base difference ...
written 14 months ago by SaltedPork100

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