Moderator: Damian Kao
Damian Kao ♦ 14k
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Bioinformatician at Janelia Research Campus.
Posts by Damian Kao
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... You also have no k-mers with frequency of 1, which is extremely unlikely. Did you somehow doubled up your input fastq? Did you copy the original fastq at some point and concatenated the copy to the original? ...
written 22 days ago by
Damian Kao ♦ 14k
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... Your bottle-neck is likely not going to be the choice of language. It's going to be the availability of existing packages to do what you want to do. Python will likely be faster for loading large datasets, but if there aren't already packages for scRNA-seq analysis, are you going to spend the time t ...
written 5 weeks ago by
Damian Kao ♦ 14k
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... I think it's supposed to be faster for short intervals? ...
written 6 weeks ago by
Damian Kao ♦ 14k
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... From what I know, the shared memory feature is used so multiple separate STAR jobs can access the same loaded genome index. So if you have relatively small amount of memory and you want to run multiple jobs, this will reduce your memory footprint.
How many separate STAR jobs are you running? Your p ...
written 8 weeks ago by
Damian Kao ♦ 14k
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... Try all of them. In my experience there isn't one method that just works all the time. Sometimes my Spades is better than my Canu. Sometimes my miniasm is better than my Spades,etc. ...
written 8 weeks ago by
Damian Kao ♦ 14k
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... Have you tried the -y parameter in gffread:
-y write a protein fasta file with the translation of CDS for each record ...
written 8 weeks ago by
Damian Kao ♦ 14k
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... Your file looks like a gtf file, not gff. And you probably want to be careful with what you mean by "first" CDS. Do you mean "first" according to genomic coordinate or "first" according to the gene? If a gene is on the minus strand of the genome, the first CDS according to the gene is actually the l ...
written 8 weeks ago by
Damian Kao ♦ 14k
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... It looks like you have a .gtf file. That means you can extract the exon lines from the .gtf file and count and sum up the exonic intervals.
You can generate a sorted .bed file of exon coordinates by:
grep -P '\texon\t' your.gtf | cut -f 1,4,5 | sort -k1,1 -k2,2n > exons.bed
You can merge t ...
written 8 weeks ago by
Damian Kao ♦ 14k
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... I recently got back a genome from Dovetail that increased N50 from ~100kb to ~50MB. Yes, that's a 500X increase in contiguity.
N50 should not be the only stat for assessing how good a genome is. But it is still pretty impressive. Gene discovery/BUSCO stats also significantly increased.
A few cavea ...
written 10 weeks ago by
Damian Kao ♦ 14k
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Comment:
C: Variant calling in genomic chunks
... Thanks for the reply. I see what you mean with the SVs and possibly even indels. I am not interested in SVs for now, but do want to preserve indel information if I can.
The BAM files I am working with are low coverage. I guess I'll to write a script to chunk the BAM file based on coverage "islands ...
written 10 weeks ago by
Damian Kao ♦ 14k
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