User: colindaven
colindaven • 930
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Posts by colindaven
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... The excellent Bioconda: sustainable and comprehensive software distribution for the life sciences (though everyone probably already read the preprint in 2017)
https://www.nature.com/articles/s41592-018-0046-7 ...
written 1 day ago by
colindaven • 930
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... Use the pacbio assembly only, and if you like map Ion torrent reads to the pacbio contigs. There is an absolutely massive difference in read length and quality between the two!
If unclear : ion torrent is pretty awful ...
written 1 day ago by
colindaven • 930
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... Very very specific question. Just try it ?
I remember from using Gmap extensively in the past it does a great job of creating GFF3 files of correctly mapped transcripts with intron exon structures which you can view in IGV JBrowse etc. Excellent.
It would also print a list of contigs which no mapp ...
written 1 day ago by
colindaven • 930
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... Is your "genome" - assembled with trinity - actually a trasncriptome assembly ? ...
written 2 days ago by
colindaven • 930
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... In terms of published data, A. Quinlans group performed a nice analysis and released the data properly for others to use. Kudos.
Data are in BED and Bigwig format so hopefully useful. You can perhaps take the inverse of the constrained regions and restrict to exons to find the regions you want (us ...
written 2 days ago by
colindaven • 930
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... Also, how many SNVs can you see directly eye-balling the raw data?
If very deep coverage, try downsampling or using the Tablet assembly browser ...
written 2 days ago by
colindaven • 930
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... Long read data will be more informative on transcript structure. See how far you get with your long read data, I've got a lot out of canu 's corrected reads.
However, SNVs and homopolymers will be an issue.
Also, maybe you can try using public data for short read correction. ...
written 2 days ago by
colindaven • 930
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... Have a look at this -
https://ewels.github.io/sra-explorer/
...
written 2 days ago by
colindaven • 930
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... Not an expert here on ONT transcriptomics, but I would suggest in addition to using canu.
- correction with short reads if possible. The tool FMLRC had a good writeup recently
- read correction using long reads with canu. The phase will be lost, but that's likely not an issue
- read mapping of ...
written 2 days ago by
colindaven • 930
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... Have a look at the quality of read 1 and read2 with FASTQC or similar (fastp ). Do the quality values of the second read drop off markedly along the read ? Try trimming ? Or as suggested above BWA.
Bad R2 is pretty common, especially on >150bp reads from some illumina sequencers. ...
written 7 days ago by
colindaven • 930
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