User: colindaven
colindaven • 740
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Posts by colindaven
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... I would just assemble the new PacBio sequences de novo, eg with Canu. I would be surprised if you didn't have 40X + coverage.
The Pacbio assembly is going to be on a different planet to your existing assembly. The Illumina data can still be used to polish the assembly errors with Racon and or Pilon. ...
written 20 hours ago by
colindaven • 740
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... Thats a really poor dataset for de novo assembly as it contains only single end reads. Also, Ion torrent data contains lots of nasty indels which cause artificial frameshifts in predicted genes. Lastly, there is no long range information.
What coverage do you have ?
I would advise you to try soap ...
written 9 days ago by
colindaven • 740
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... That was not really informative enough to help any further. Just a recommendation anyway. ...
written 11 days ago by
colindaven • 740
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... To answer one part of your question, there is a graphical blast web client which can be easily installed locally using docker. It is still a bit buggy though. It may also be able to index your sequence properly, not sure what your issue is there really.
https://github.com/wurmlab/sequenceserver
...
written 15 days ago by
colindaven • 740
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... In my experience, no. Fat nodes with lots of RAM are required. I wouldn't generally attempt vertebrate short read assembly on a machine with lower than 128 GB RAM, better 512 GB. ...
written 22 days ago by
colindaven • 740
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... How long is "forever ?" ...
written 22 days ago by
colindaven • 740
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Answer:
A: De novo assembly programm
... As the above commenters mention, a large genome is not going to be assembled well with just paired end short read data. You'll need a good set of mate paired aka long jumping distance reads to go with it if you stick with Illumina.
However I would really recommend a long read library and going for ...
written 26 days ago by
colindaven • 740
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Answer:
A: plant long non-coding RNA
... Here's a couple, but as far as I remember not many are plant specific
https://academic.oup.com/nar/article/45/22/e183/4282667
https://www.lncrnablog.com/uclncr-ultrafast-and-comprehensive-long-non-coding-rna-detection-from-rna-seq-2/
...
written 29 days ago by
colindaven • 740
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... I used Shrimp2 for SOLiD back in the day I believe (2011). Pretty poor. mrFAST was far, far worse. We should be very glad to have tools like bwa, STAR, and bowtie2. Just my two cents. Novoalign allows a lot of parameter tuning, but is commercial.
Segemehl http://hoffmann.bioinf.uni-leipzig.de/LIFE/s ...
written 5 weeks ago by
colindaven • 740
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... I'm no expert with HGAP4, but why not try an alternative assembler such as Canu. At least you'll have something to compare to. Also, if you have a diploid organism you might get some haplotype information out of the advanced Canu functions similar to Falcon's Unzip principle. This might resolve your ...
written 5 weeks ago by
colindaven • 740
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