Counting softmasked bases in a FASTA

Question

[Timotheus]

Hello,

I've got a softmasked assembly (FASTA) that I will filter in various ways (e.g., remove/truncate contigs). How could I count the number of softmasked bases at the end? Thought toolkits like bioawk or seqkit could be helpful, but didn't find a solution.

Thanks in advance!

Answer 1

[Pierre Lindenbaum]

grep -v '^>' in.fa |  tr -d --complement 'atgc'  | wc -c

[Pierre Lindenbaum]

ah sorry, I didn't see the "..at the end"

Answer 2

[Matthias Zepper]

It would have been helpful, if you had provided a sample, but I presume you are thinking of something like this:

>chr1
AAAAAaatttaccCCCtagatgaCCCCCCCGCTACTGGGGGGGGGGGGGGgggtaacatcaaat

And now you would like to count exclusively the number of softmasked based at the 3' prime end?

Your idea using seqkit was actually pretty good...

seqkit locate -p "[acgtn]+$" -r -P example.fasta

will return

seqID   patternName pattern strand  start   end matched
chr1    [acgtn]+$   [acgtn]+$   +   51  64  gggtaacatcaaat

which you can pipe to awk to count the length:

seqkit locate -p "[acgtn]+$" -r -P example.fasta | awk 'NR>1{print $1,$6-$5}'

[Timotheus]

My apologies: by 'at the end' I meant after the different filtering steps. I added this because I know the proportion of originally masked bases from Repeat Masker output. Sorry for not being clearer!