User: Jeffin Rockey
Jeffin Rockey • 1000
- Reputation:
- 1,000
- Status:
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- Location:
- Karimannoor
- Last seen:
- 4 days, 9 hours ago
- Joined:
- 2 years, 8 months ago
- Email:
- j***********@hotmail.com
Posts by Jeffin Rockey
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Comment:
C: ddRAD analysis pipelines
... Stacks issue I could not resolve.
ipyrad issue root cause was wrong cut site information given which I corrected. ...
written 4 days ago by
Jeffin Rockey • 1000
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... Check the separators. MT is there in EHMT1 . Is the bed made in a Windows machine or so?
If so dos2unix might help
Also what about *GRCh38.dna.primary_assembly.Genome_File.txt* ?
...
written 8 weeks ago by
Jeffin Rockey • 1000
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... It should be just that the bed file has mitochondria entry whereas the genome file do not have an entry regarding that. ...
written 8 weeks ago by
Jeffin Rockey • 1000
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235
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... single read below a threshold or it is single base (in title)? ...
written 10 weeks ago by
Jeffin Rockey • 1000
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... The error 139 related bug that existed before is supposed to be fixed in the bowtie2 version 2.3.4.3 that you are using.
However, if you have time to try something which holds a very remote chance of being right, please go back three versions and rerun the same script with bowtie2 v2.3.4 in which a ...
written 11 weeks ago by
Jeffin Rockey • 1000
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... Very odd. Command seems fine. If you want to try a different tool use sambamba. ...
written 12 weeks ago by
Jeffin Rockey • 1000
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... Please share the exact flank command used. ...
written 12 weeks ago by
Jeffin Rockey • 1000
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... What is the snippet pasted? ...
written 12 weeks ago by
Jeffin Rockey • 1000
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... Could you please check if counting by reads rather than by pairs is working fine. i.e.
Please use flag -F 260 instead of 12 to get mapped count.Also -f 4 instead of 12 to get unmapped.
Please add the above two and see if it totals correctly with input count.
example
samtools view -bhS aln-mt. ...
written 12 weeks ago by
Jeffin Rockey • 1000
1
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1
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173
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... Could you please share the commands used to calculate mapped & unmapped. And also the aligner used with parameters given. ...
written 12 weeks ago by
Jeffin Rockey • 1000
Latest awards to Jeffin Rockey
Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Centurion
12 weeks ago,
created 100 posts.
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Good Answer
10 months ago,
created an answer that was upvoted at least 5 times.
For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
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