User: colindaven
colindaven • 280
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Posts by colindaven
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... I don't have a problem with docker usage and appreciate all the work which has gone into packaging this tool up nicely. I will give installation a go when I get a chance.
For those struggling with docker, other container software does exist. Check out singularity for example, though I think it is e ...
written 5 hours ago by
colindaven • 280
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... Any idea on the maximum number of SNPs this has been tested with ? Eg 2-10m SNVs from WGS data would be of interest to my users. ...
written 5 hours ago by
colindaven • 280
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... This is a complex topic. You can do GC normalization, library size normalization and so on.
Here is a good paper on the topic which may help.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165015
...
written 22 hours ago by
colindaven • 280
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Answer:
A: denovo pacbio assembly
... Canu did not find any reads. Check whether the file ~/canu/pacbio.fastq is present and contains reads.
Also check using "less pacbio.fastq" if the read file is ok and contains enough reads to do the autocorrection step (should be fairly large, i.e. more than 50 -100 MB I would guess).
Good luck.
...
written 22 hours ago by
colindaven • 280
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... This is a very specific biological question. I would guess the ability to detect SNPs would be strongly affected by the number of transcripts expressed in each individual. I don't think anyone here can provide you with a definitive answer, the best bet would be to go through other non-model organism ...
written 13 days ago by
colindaven • 280
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... Interesting. I don't know of any magic numbers.
Instead of comparing assemblies directly, which would always ignore heterozygote variation (assemblies are likely to be haploid), I would suggest another approach.
- a) merge assemblies. Software: cd-hit, supertranscript
- b) rename contigs in merg ...
written 14 days ago by
colindaven • 280
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... True, but it would be even easier to just use head instead of wc -l and sed.
> egrep -n -m 1 '##FASTA' test.gff
> head -n 15 test.gff > result.gff
...
written 19 days ago by
colindaven • 280
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... Does your reference sequence have chromosome names like "11" and not chr11 ? ...
written 4 weeks ago by
colindaven • 280
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Answer:
A: NCI-60 RNA-seq data
... Looks like it is controlled access. I checked on the EBI ENA too, which make FASTQ files available, but no options there either. Contact the project manager or check the publication for details ? ...
written 5 weeks ago by
colindaven • 280
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... Save yourself some time and nerves: install bioconda
https://bioconda.github.io/recipes.html#recipes
Then type
conda install randfold ...
written 5 weeks ago by
colindaven • 280
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