User: marongiu.luigi
marongiu.luigi • 360
- Reputation:
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- Germany, Mannheim, UMM
- Last seen:
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- 3 years, 2 months ago
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Posts by marongiu.luigi
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... I will, but it might take sometimes... ...
written 2 days ago by
marongiu.luigi • 360
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... same thing when i changed the shebang to `#!/usr/bin/env python2
` ...
written 3 days ago by
marongiu.luigi • 360
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... I ran: `$ ~/src/freebayes/scripts/frebayes-parallel <(python2 ~/src/freebayes/scripts/fasta_generate_regions.py ~/refSeq/fusion/fusion38-10k.fa.fai) 36 -f ~/refSeq/fusion/fusion38-10k.fa ~/servers/chirexpsrv3_a32/LUIGI_HIPO32_nls/rslt/A1/A1-N_F-AlnSrtDed.bam > ~/Downloads/h32/rslt/A1-N_F.vcf` ...
written 3 days ago by
marongiu.luigi • 360
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... I thought I did it by launching freebayes-parallel with its absolute path... ...
written 3 days ago by
marongiu.luigi • 360
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... I think the standard is Python 3.7.0 because this is what comes out if I type `python` on the terminal ...
written 3 days ago by
marongiu.luigi • 360
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... Dear all,
I would like to run freebayes as a multi-thread application. I followed the script given as an example
freebayes-parallel < (fasta_generate_regions.py ref.fa.fai 100000) 36 -f ref.fa aln.bam > out.vcf"
by writing a command:
pathTo/freebayes/scripts/frebayes-parallel <(p ...
written 3 days ago by
marongiu.luigi • 360
• updated
48 minutes ago by
RamRS ♦ 20k
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Comment:
C: install Primer3 on Ubuntu
... It worked for me! Thanks
...
written 5 weeks ago by
marongiu.luigi • 360
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... I tried to investigate but none of the steps introduced funny characters. It will remain a mistery... ...
written 8 weeks ago by
marongiu.luigi • 360
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... The alignment has started! So the problem was indeed about those faulty characters. Case closed. Thank you so much again. ...
written 9 weeks ago by
marongiu.luigi • 360
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... Ah, that is very clever!
Yes it did find some troubles:
$ awk '/[^a-zA-Z]/ && $0 !~"^>" {print "invalid char at line ", NR}' fusion38-10k.fa
invalid char at line 44558934
invalid char at line 46471885
$ sed '44558934q;d' fusion38-10k.fa
TGCTTAGATGTAAGAGATAAACATTTAAA ...
written 9 weeks ago by
marongiu.luigi • 360
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