User: Ric

gravatar for Ric
Ric180
Reputation:
180
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Trusted
Location:
Australia
Last seen:
2 days, 4 hours ago
Joined:
6 years, 6 months ago
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m*******@gmail.com

Posts by Ric

<prev • 128 results • page 1 of 13 • next >
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SparseAssembler inward or outwards reads
... Hello, How can I determine whether my reads are inward or outward paired-end reads? Thank you in advance. Michal ...
assembly written 10 days ago by Ric180 • updated 10 days ago by h.mon16k
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5 follow
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local web BLAST server
... Hello, I look for a local web BLAST server which I could set up for our group. Is there any which support to submit jobs and when the results ready is the user gets an email notification? Thank you in advance ...
blast written 18 days ago by Ric180 • updated 17 days ago by lieven.sterck1.9k
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Comment: C: Hybrid assembly of PacBio and Illumina reads
... How would you use mate-pairs reads after DBG2OLC? ...
written 25 days ago by Ric180
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How to circularize genome assemblies
... Hi, are there any tools which can circularize genome PacBio assemblies/reads? I have an assembly created by miniasm and Racon. Thank you in advance. ...
genome assembly written 12 weeks ago by Ric180 • updated 9 weeks ago by Ezra Kitson10
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PacBio sequence lengths distribution
... Hi, How is it possible to get sequence lengths distribution out of PacBio's Sequel BAM files? Thank you in advance. ...
sequence pacbio sequencing written 4 months ago by Ric180 • updated 4 months ago by WouterDeCoster30k
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How to use DASCRUBBER pipeline for PacBio
... Hi, I was able to follow the first [4 steps][1] of the DASCRUBBER [pipeline][2] but I am not sure how to do 5 - 8 steps. 5. `DASmap [-p] [ | ... ]`. What are ` |`? 6. `DASrealign [-v] [-l] `. What are -l option, ` `, `source:las` and `target:las`? 7. `REPqv ....` Is subjet:db the ...
assembly pacbio sequencing written 5 months ago by Ric180
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(Closed) finding silenced genes
... Hi, How to find genes which are silenced between transcript and genome assembly? Thank you in advance. ...
gene assembly written 6 months ago by Ric180
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Answer: A: comparing annotations between genomes.
... Thank you, but I still not sure which files should have I to use? ls input.cds.fa input.gff lifted_cleaned.cds.fa lifted_cleaned.gff lifted.gff3 unlifted.gff3 unmapped.txt > grep "ID=" unlifted.gff3 | wc -l 19233 > grep "ID=" lifted_cleaned.gff | wc -l 33639 ...
written 6 months ago by Ric180
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Comment: C: splitting daligner jobs
... Hi, I got many `daligner: Track 'dust' annotation file is junk` with the following commands DBsplit -x500 -s200 DB DBdust DB HPC.daligner DB -T8 -mdust -H6973 I wrote the following script to submit each command from `test.01.OVL` parallel. #!/bin/bash while IFS='' read ...
written 6 months ago by Ric180
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comparing annotations between genomes.
... Hi, I used [flo][1] which did a mapping of annotations from one genome assembly to another. The flo developer did on their page the following calculation: > For an ant genome (~350 Mb) we saw 90% annotations map identically to the new assembly (unpublished result). How did they calculate the ab ...
annotation gff crossmap liftover written 7 months ago by Ric180

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Scholar 10 months ago, created an answer that has been accepted. For A: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
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