User: Jeffin Rockey
Jeffin Rockey • 1.1k
- Reputation:
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- Karimannoor
- Last seen:
- 5 days, 15 hours ago
- Joined:
- 3 years, 4 months ago
- Email:
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Posts by Jeffin Rockey
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... awk -F$'\t' -v OFS="\t" '{split($4,fourth,":");split($6,sixth,":");print $1,$2,$3,fourth[1],$5,sixth[1]}' df.bed ...
written 8 weeks ago by
Jeffin Rockey • 1.1k
• updated
8 weeks ago by
finswimmer ♦ 12k
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... Hi Ole,
Could you please point me to some link or so which would help me understand the {},::: etc. ...
written 7 months ago by
Jeffin Rockey • 1.1k
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... Are you sure the bowtie2-build completed successfully prior to attempting align?
*2.bt2l seems to be of 0 size. ...
written 7 months ago by
Jeffin Rockey • 1.1k
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... Install bowtie2 and use *bowtie2-build* to build index. It will automatically build **.bt2l** indices for wheat. ...
written 7 months ago by
Jeffin Rockey • 1.1k
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... Hi Malcom,
The suggested command appears to be super efficient, even though I did not understand many of the usages.
Can you please explain the {=s/.new.vc$f//=}, {}, ::: etc ...
written 7 months ago by
Jeffin Rockey • 1.1k
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... Hi Pierre,
I did not understand. Would bcftools view do any replacement ? ...
written 7 months ago by
Jeffin Rockey • 1.1k
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... Changing ***1s|*** to simply ***s|*** will do replacements for all *Sample1* occurrences. ...
written 7 months ago by
Jeffin Rockey • 1.1k
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... In bash this should do.
for i in *.new.vcf
do
ID_NAME=$(basename "$i" .new.vcf)
sed -i "1s|Sample1|$ID_NAME|g" $i
done
Caution: I have used -i with sed. So the actual files will get edited in place.
Now added 1s also as to limit the replacement to first line ...
written 7 months ago by
Jeffin Rockey • 1.1k
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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 8 months ago by
Jeffin Rockey • 1.1k
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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 9 months ago by
Jeffin Rockey • 1.1k
Latest awards to Jeffin Rockey
Supporter
6 months ago,
voted at least 25 times.
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: bedtools getfasta for mm9 genome
Guru
7 months ago,
received more than 100 upvotes.
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Centurion
10 months ago,
created 100 posts.
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Good Answer
18 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
19 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Appreciated
23 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
2.2 years ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
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