Moderator: 5heikki
5heikki ♦ 8.4k
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Posts by 5heikki
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... https://www.biostars.org/p/144569/ ...
written 4 weeks ago by
5heikki ♦ 8.4k
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Comment:
C: Rename fasta headers from CSV
... Do the fasta files have linebreaks in seqs? If not, then perhaps e.g.
join -1 1 -2 1 -t $'\t' \
<(sed 's/,/\t/' file.csv | sort -k1,1) \
<(paste - - //' | sort -k1,1) \
| awk 'BEGIN{FS="\t"}{print ">"$2"_"$3"\n"$4}' ...
written 8 weeks ago by
5heikki ♦ 8.4k
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Comment:
C: intersection for several file
... If by intersection OP means that the line has to be in every file, then the above does not work..
However (the same than JC's answer really)..
cat file* | sort | uniq -c | awk '{if($1==6){print $2}}'
...
written 8 weeks ago by
5heikki ♦ 8.4k
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... Extract your gene of interest +/- 10k bp region from a large number of reference genomes of your species. Do they align nicely? If yes, that region is conserved across your species. Now map your reads against this region. In case you see something like "|||||||||||||.....|||||||||||||||" (with pipes ...
written 10 weeks ago by
5heikki ♦ 8.4k
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... Another thing you can do is to pick a reference genome that is the closest to your sequenced genome. Then you map the reads from your genome on the reference genome and see what is missing (other than your gene of interest that is).. ...
written 10 weeks ago by
5heikki ♦ 8.4k
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... I haven't done any wetlab stuff for a very long time, but IMO starting from a cell culture, it would take extraordinary skill to somehow manage to extract the DNA covering just 50% of some prokaryotic genome.. ...
written 10 weeks ago by
5heikki ♦ 8.4k
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... I don't know about eukaryote genomes, but I disagree with that you can have high coverage, few contig, high N50 prokaryote genome assembly (you defined bacteria in OP) and still miss a considerable part of the genome. "Hundreds of genes" is less than 1% of all genes in the context of your typical ma ...
written 10 weeks ago by
5heikki ♦ 8.4k
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... IMO if you have +20X coverage for your contigs and the assembly is of decent quality (~100 contigs or less, N50 > 50k) and blastn returns nothing, then conclusion is that the sequenced organism does not have that specific gene ...
written 10 weeks ago by
5heikki ♦ 8.4k
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Answer:
A: FastQC results interpretation
... Try [FASTQE][1]
[1]: https://fastqe.com/ ...
written 11 weeks ago by
5heikki ♦ 8.4k
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... Why do people ask questions without providing any background information whatsoever? ...
written 3 months ago by
5heikki ♦ 8.4k
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