User: wocana
wocana • 10
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Posts by wocana
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Answer:
A: Orthomcl clusters to fasta
... Thx you all at the end first i modified and then used lieven.sterck command
grep 'cluster000:' | sed 's/cluster000://' | sed 's/ /\n/g' > ids2get.lst
and then the script runned correctly
#!/usr/bin/env perl
my $list_file = $ARGV[0];
my $fasta_in = $ARGV[1];
my $fasta_ ...
written 9 months ago by
wocana • 10
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Comment:
C: Orthomcl clusters to fasta
... Didnt work
Error: [blastdbcmd] CoGr|NW_001583259.1:530924..534690: OID not found
Error: [blastdbcmd] CoGr|NC_008801.1:39070112..39072248: OID not found
Error: [blastdbcmd] CoGr|NC_008801.1:104399108..104402881: OID not found
Error: [blastdbcmd] CoGr|NC_008801.1:127199820..127202817: ...
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415
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Comment:
C: Orthomcl clusters to fasta
... The cluster im interest of has 260 fasta IDs and i wanna extract them from the fasta file, first i organaized them
1 ID per line as you can see below "list.txt". Im using that script i modified it but its not working at all ...
written 10 months ago by
wocana • 10
0
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415
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2
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Comment:
A: Orthomcl clusters to fasta
... im using this script but im just getting 136/260 i dont know why.. my list.txt look like this
CoGr|NW_001584579.1:68053..71823
CoGr|NC_008804.1:48922615..48926373
CoGr|NC_008801.1:545795465..545799243
CoGr|NC_008804.1:161966386..161970130
CoGr|NC_008807.1:226381677..226385438 ...
written 10 months ago by
wocana • 10
4
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415
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5 follow
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... Any idea how to extract orthomcl Clusters to fasta?
I got 540 clusters i just want some of them on fasta.
The final output results like this:
cluster000: Ratn|NC_000067.6:7605211..7607094 Ratn|NC_000076.6:46984187..46986072 Ratn|NC_000072.6:126135324..126137210 Ratn|NC_000071.6:43059052.. ...
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... When i run this on orthomcl (running 39 proteomes):
/home/intirules/Desktop/Tesis/orthomclSoftware-v2.0.9/bin/orthomclPairs /home/intirules/Desktop/Tesis/orthomclSoftware-v2.0.9/doc/OrthoMCLEngine/Main/orthomcl.config.template ../orthomcl_pairs.log cleanup=yes
I get this error
DBD::mysql: ...
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374
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Answer:
A: GFF3 to fasta (error)
... awk '{if ($1~/[0-9]+/) print $10"\t"$1}' Muschr4.fsa.mod.pass.list > Muschr4.fsa.mod.pass.list.extract
perl $path/LTR_retriever/bin/call_seq_by_list.pl Muschr4.fsa.mod.pass.list.extract -C Muschr4.fsa.mod > Muschr4.fsa.mod.pass.list.extract.fa
This solved it ...
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Comment:
A: GFF3 to fasta (error)
... intirules@Biointi:~/Desktop/Tesis/Secuencias/PruebaRetriever$ grep ">" Muschr4.fsa | head -10
>NC_000070.6 Mus musculus strain C57BL/6J chromosome 4, GRCm38.p4 C57BL/6J
intirules@Biointi:~/Desktop/Tesis/Secuencias/PruebaRetriever$ grep ">" Muschr4.fsa | grep "seq0"
...
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... Hi im trying to extract some sequences from my GFF3 file to fasta but when i run this:
$ bedtools getfasta -fi Muschr4.fsa -bed Muschr4.fsa.mod.pass.list.gff3 -fo ERVCom.fa
I get
WARNING. chromosome (seq0) was not found in the FASTA file. Skipping.
WARNING. chromosome (seq0) was ...
written 13 months ago by
wocana • 10
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