User: Ric
Ric • 180
- Reputation:
- 180
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- Trusted
- Location:
- Australia
- Last seen:
- 4 weeks, 1 day ago
- Joined:
- 6 years, 4 months ago
- Email:
- m*******@gmail.com
Posts by Ric
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... 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.
...
written 29 days ago by
Ric • 180
• updated
4 days ago by
Ezra Kitson • 10
1
vote
1
answer
124
views
1
answer
... Hi, How is it possible to get sequence lengths distribution out of PacBio's Sequel BAM files?
Thank you in advance. ...
written 11 weeks ago by
Ric • 180
• updated
11 weeks ago by
WouterDeCoster ♦ 28k
0
votes
0
answers
177
views
0
answers
... 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 ...
written 3 months ago by
Ric • 180
0
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0
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182
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... Hi,
How to find genes which are silenced between transcript and genome assembly?
Thank you in advance. ...
written 4 months ago by
Ric • 180
0
votes
2
answers
246
views
2
answers
... 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 4 months ago by
Ric • 180
0
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2
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296
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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 4 months ago by
Ric • 180
0
votes
2
answers
246
views
2
answers
... 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 ...
written 5 months ago by
Ric • 180
0
votes
2
answers
296
views
2
answers
Comment:
C: splitting daligner jobs
... Hi, in the meantime I started to split the database with the following command:
DBsplit -x500 -s200 plantDB
DBdust plantDB
It created the following files:
-rw-rw---- 1 lorencm Waterhouse_Team 476M Dec 18 15:23 .plantDB.idx
-rw-rw---- 1 lorencm Waterhouse_Team 23K Dec 18 1 ...
written 5 months ago by
Ric • 180
0
votes
0
answers
354
views
0
answers
Comment:
C: PacBio reads polishing
... Yes, I try to do an assembly.
On our cluster CANU makes always some problems to run and FALCON completely is not working. ...
written 5 months ago by
Ric • 180
0
votes
0
answers
354
views
0
answers
Comment:
C: PacBio reads polishing
... Yes, I try to do an assembly.
On our cluster CANU makes always some problems to run and FALCON completely is not working. ...
written 5 months ago by
Ric • 180
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