Moderator: Damian Kao
Damian Kao ♦ 14k
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Bioinformatician at Janelia Research Campus.
Posts by Damian Kao
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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 21 hours 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 22 hours 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 23 hours 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 1 day 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 days 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 days ago by
Damian Kao ♦ 14k
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... Is variant calling done on a per-position basis? I've read recommendations to split the BAM file by chromosomes and parallel call the chromosomes for speed
Could I further segment each chromosome into chunks and do calling on each chunk? For example if I: 1) Split a chromosome into 1MB segments. 2) ...
written 10 days ago by
Damian Kao ♦ 14k
• updated
10 days ago by
finswimmer • 1.4k
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... I've used GAM-NGS in the past with some success:
https://github.com/vice87/gam-ngs ...
written 11 days ago by
Damian Kao ♦ 14k
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... That pipeline might be a bit old. I don't think you need to do the realignment target creater/realign for indel anymore as haplotypeCaller will do that now.
The general steps for me are:
1. trim reads
2. bwa mem align to genome
3. mark duplicates
4. use HaplotypeCaller to generate gvcf
5. Combine ...
written 16 days ago by
Damian Kao ♦ 14k
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Comment:
C: Stringtie to DESeq2
... Can you paste a few lines of your phenotype_2.txt?
**EDIT
nevermind, look at Kevin's response below. You are using Python3+ and the script is meant for python2.7. ...
written 16 days ago by
Damian Kao ♦ 14k
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