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2 answers
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How to add corresponding "chr" before location (start, end) of bed alike file?

I have some bed alike files but don't have chr term in the fisrt column, that I want to add chr and its corresponding chromosome ...
Deb's user avatar
  • 289
1 vote
2 answers
121 views

How to visualize FIMO outputs?

I used FIMO to scan several of my promoter sequences for TF binding motifs. The output .tsv file gives me the motif name/sequence plus the start and stop location, how can I visualize these outputs to ...
JohnDoe23's user avatar
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2 answers
87 views

How to calculate average from a column when consecutive cells are similar in different columns?

I wonder how can I calculate the average of column 7 (WPS_win) when consecutive cells in column 2, column 3, and column 1 are the same. The file is in bed format (tab-separated format). The original ...
Deb's user avatar
  • 289
1 vote
3 answers
259 views

How to join multiple large .tsv (> 20 GB, bed file) files by two identifier?

This question has also been asked on Biostars I wonder how can I join multiple large .tsv files (over 20 GB each) by using two identifiers (columns) which I used to do using the ...
Deb's user avatar
  • 289
2 votes
1 answer
153 views

Improving conversion of abricate tsv file to gff3 file

Since such a neat solution (abricate tsv to gff3) was provided by Steve, here are few other steps that I am looking to add so that the script progress to logical maturity to be usable by many others. ...
com's user avatar
  • 31
1 vote
1 answer
90 views

Convert Abricate output tsv file to gff3 format

I have a tsv file generated from abricate (https://github.com/tseemann/abricate). I need to convert them to gff3 format with certain columns retained, certain columns reordered, while other columns ...
com's user avatar
  • 31
2 votes
2 answers
164 views

Sort dictionary in descending order

Hi I am looking to sort a list of kmers into descending order. I used KMC to obtain a list of kmers from a fastq file separated by tab (e.g.; kmer count). From there I have written this python script ...
rimo's user avatar
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