User: Ric

gravatar for Ric
Ric180
Reputation:
180
Status:
Trusted
Location:
Australia
Last seen:
4 weeks, 1 day ago
Joined:
6 years, 4 months ago
Email:
m*******@gmail.com

Posts by Ric

<prev • 125 results • page 1 of 13 • next >
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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 29 days ago by Ric180 • updated 4 days 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 11 weeks ago by Ric180 • updated 11 weeks ago by WouterDeCoster28k
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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 3 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 4 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 4 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 4 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 5 months ago by Ric180
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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 Ric180
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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 Ric180
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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 Ric180

Latest awards to Ric

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Popular Question 11 weeks ago, created a question with more than 1,000 views. For estimate genome coverage
Popular Question 6 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Centurion 6 months ago, created 100 posts.
Great Question 7 months ago, created a question with more than 5,000 views. For Fastqc And Require Tools
Scholar 8 months ago, created an answer that has been accepted. For A: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
Popular Question 9 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Popular Question 11 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Popular Question 12 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Great Question 17 months ago, created a question with more than 5,000 views. For Ignore Reads In Bwa
Popular Question 17 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Popular Question 2.6 years ago, created a question with more than 1,000 views. For How to find out codon changes in non-synonymous and synonymous SNPs
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Ignore Reads In Bwa
Appreciated 4.0 years ago, created a post with more than 5 votes. For Fastqc And Require Tools
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Ignore Reads In Bwa
Student 6.1 years ago, asked a question with at least 3 up-votes. For Fastqc And Require Tools

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