User: genomes_and_MGEs

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Posts by genomes_and_MGEs

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Extract protein files from nucleotide accession numbers
... Thanks for the reply. Your solution works well, but it outputs tons of proteins with no link to the chromosome. I would like to link the extracted proteins to the chromosome. Any solution? ...
written 3 months ago by genomes_and_MGEs0
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Comment: C: Batch rename protein fasta headers
... Thanks for the reply. The thing is that I have multiple files to use as input. So, I guess using a loop to create a renamed output for each file would be better. Do you think you can help me with this? Usually for DNA sequences, I use for F in *.fasta; do N=$(basename $F .fasta) ; bbrename.sh in=$F ...
written 3 months ago by genomes_and_MGEs0
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Extract protein files from nucleotide accession numbers
... Hey everyone, I would like to extract all proteins, using a list of nucleotide accession numbers as input. For example, considering the `list.txt` with the following accessions: NC_008803.1 NCVQ01000001.1 NC_039364.1 NC_005101.4 I would like to extract the protein files for all co ...
sequence written 3 months ago by genomes_and_MGEs0 • updated 3 months ago by vkkodali2.0k
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Batch rename protein fasta headers
... Hey guys, I have tons of protein multi-fasta files and I would like to append the name of the file to the fasta-headers. For example, for a input file one.txt with the headers >1 ATGC... >2 ATGCAT... I would like to have the output >one_1 ATGC... >one_2 ...
sequence written 3 months ago by genomes_and_MGEs0 • updated 3 months ago by Joe17k
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Extract fasta sequnces not matching a list
... Hey guys, I know it's possible to use seqtk subseq to extract fasta files matching a list. Now, is there a way to extract those fasta files that don't match the exact fasta headers on the list? Thanks! ...
assembly sequence written 4 months ago by genomes_and_MGEs0 • updated 4 months ago by genomax85k
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(Closed) Move files that match the names on a list
... Hey everyone, I have a directory with several files, and I would like to move the files that match the name in a given list to another directory. Can you help me out with this? Thanks! ...
genome sequence written 11 months ago by genomes_and_MGEs0 • updated 11 months ago by 160
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List names in column that match a given word in another column
... Hey guys, I would like to list all lines in column 1 that match a given expression in column 3. For example, 1 2 3 A B C D E F G H C ... So, I would like to list A and G, because they match the C on column 3. Btw, the match in column 3 has spaces! Thank you! ...
genome sequence written 11 months ago by genomes_and_MGEs0 • updated 11 months ago by genomax85k
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Comment: C: Kill nohup bash process
... It doesn't work, because the PID is always changing on the server... So, I found a solution: pkill -STOP -P the_ppid Thanks anyway guys! ...
written 13 months ago by genomes_and_MGEs0
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Kill nohup bash process
... Hey guys, I ran this nohup bash -c 'for next in $(cat all_bacteria_links.txt); do wget -P all_bacteria "$next"/*genomic.fna.gz; done', and now I want to kill the process. I ran the command in ssh server, so whenever I try to kill PID or kill -9 PID, the server connection closes. Can you ple ...
genome sequence written 13 months ago by genomes_and_MGEs0 • updated 13 months ago by Santosh Anand5.1k
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Comment: C: Download genomes within a given GC content interval
... Thanks, really appreciate that! ...
written 13 months ago by genomes_and_MGEs0

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Popular Question 11 months ago, created a question with more than 1,000 views. For Kill nohup bash process

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