User: Ric

gravatar for Ric
Ric180
Reputation:
180
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Location:
Australia
Last seen:
2 weeks ago
Joined:
6 years, 1 month ago
Email:
m*******@gmail.com

Posts by Ric

<prev • 123 results • page 1 of 13 • next >
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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 18 days 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 weeks 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 weeks 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 7 weeks 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 For an ant genome (~350 Mb) we saw 90% annotations map identically to the new assembly (unpublished result).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 9 weeks 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 9 weeks 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 9 weeks 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 9 weeks ago by Ric180
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PacBio reads polishing
... Hi, I ran dextractor (https://github.com/thegenemyers/DEXTRACTOR) and it generated X.subreads.arrow and a FASTA file. How could I polish the reads before the assembly? Thank you in advance. ...
assembly pacbio written 10 weeks ago by Ric180
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splitting daligner jobs
... Hi, I would like to run HINGE assembler (https://github.com/HingeAssembler/HINGE). However, I just wonder wether the neccerry steps (https://github.com/HingeAssembler/HINGE/blob/master/demo/NCTC9657_demo/run.sh) could be splitted and run on different computers and later merged? fasta2DB NCTC965 ...
assembly hinge daligner pacbio written 10 weeks ago by Ric180 • updated 9 weeks ago by govinda.kamath0

Latest awards to Ric

Popular Question 3 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Centurion 4 months ago, created 100 posts.
Great Question 4 months ago, created a question with more than 5,000 views. For Fastqc And Require Tools
Scholar 5 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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Popular Question 9 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Great Question 14 months ago, created a question with more than 5,000 views. For Ignore Reads In Bwa
Popular Question 14 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools
Popular Question 2.3 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 2.3 years ago, created a question with more than 1,000 views. For Ignore Reads In Bwa
Appreciated 3.7 years ago, created a post with more than 5 votes. For Fastqc And Require Tools
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