User: wocana

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wocana20
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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 22 months ago by wocana20
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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: ...
written 22 months ago by wocana20 • updated 22 months ago by genomax87k
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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 22 months ago by wocana20
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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 22 months ago by wocana20
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Orthomcl clusters to fasta
... 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.. ...
ortho mcl alignment cluster fasta written 22 months ago by wocana20 • updated 22 months ago by RamRS28k
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DBD::mysql::st execute failed: The table 'InplgOrthoInplg
... 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: ...
ortho ubuntu mysql orthomcl bioinformatics written 2.1 years ago by wocana20 • updated 2.1 years ago by RamRS28k
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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 $path/LTR_retriever/bin/call_seq_by_list.pl Muschr4.fsa.mod.pass.list.extract -C Muschr4.fsa.mod > Muschr4.fsa.mod.pass.list.extract.fa This solved it ...
written 2.1 years ago by wocana20 • updated 2.1 years ago by genomax87k
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Comment: A: GFF3 to fasta (error)
... intirules@Biointi:~/Desktop/Tesis/Secuencias/PruebaRetriever$ 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" ...
written 2.1 years ago by wocana20 • updated 2.1 years ago by genomax87k
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GFF3 to fasta (error)
... 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 ...
gff3 fasta extract file written 2.1 years ago by wocana20

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