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Lisa K. Johnson johnsolk

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johnsolk / example_gff3_dammit_output
Last active March 13, 2017 22:39
dammit_annotations_parsing
##gff-version 3.2.1
Transcript_0 transdecoder CDS 1664 2062 . + . ID=cds.Transcript_0|m.1;Parent=Transcript_0|m.1
Transcript_0 transdecoder exon 1 2064 . + . ID=Transcript_0|m.1.exon1;Parent=Transcript_0|m.1
Transcript_0 transdecoder five_prime_UTR 1 1663 . + . ID=Transcript_0|m.1.utr5p1;Parent=Transcript_0|m.1
Transcript_0 transdecoder gene 1 2064 . + . ID=Transcript_0|g.1;Name=ORF%20Transcript_0%7Cg.1%20Transcript_0%7Cm.1%20type%3A3prime_partial%20len%3A134%20%28%2B%29
Transcript_0 transdecoder mRNA 1 2064 . + . ID=Transcript_0|m.1;Parent=Transcript_0|g.1;Name=ORF%20Transcript_0%7Cg.1%20Transcript_0%7Cm.1%20type%3A3prime_partial%20len%3A134%20%28%2B%29
Transcript_0 transdecoder three_prime_UTR 2063 2064 . + . ID=Transcript_0|m.1.utr3p1;Parent=Transcript_0|m.1
Transcript_100002 transdecoder CDS 1 1047 . + . ID=cds.Transcript_100002|m.114344;Parent=Transcript_100002|m.114344
Transcript_100002 transdecoder CDS 1411 1722 . + . ID=cds.Transcript_100002|m.114346;Parent=Transcript_100002|m.114346
Transcript_100002
@johnsolk
johnsolk / git_error_solution.md
Created August 29, 2016 03:40
git error, fatal: HTTP request failed

Got this error message:


[ljcohen@dev-intel16 Porites_astreoites_larvae_salinity]$ git push origin master
error: The requested URL returned error: 403 Forbidden while accessing https://github.com/ljcohen/Porites_astreoites_larvae_salinity.git/info/refs

fatal: HTTP request failed

Googled problem and found this:

@johnsolk
johnsolk / formatting_annotations.sh
Created August 29, 2016 01:53
formatting transcriptome annotations for merging with lists of differentially expressed lists contig ID
sed 's_|_-_g' uniprot_sprot.blastx.outfmt6.sig > uniprot_sprot.blastx.outfmt6.fixed.sig
cut -f 1,2,17 uniprot_sprot.blastx.outfmt6.fixed.sig > uniprot_sprot.blastx.outfmt6.fixed.genes.sig
touch uniprot_P_ast_annotations_mansour_hits100DE.tab
for i in $(cut -f 2 P_ast_RNAseq_25pptv35ppt_top100DE.tab); do grep ${i/_/-} uniprot_sprot.blastx.outfmt6.fixed.genes.sig >> uniprot_P_ast_annotations_mansour_hits100DE.tab; done
sed 's/\-/\_/1' uniprot_P_ast_annotations_mansour_hits100DE.tab > uniprot_P_ast_annotations_mansour_hits100DE.fixed.tab
@johnsolk
johnsolk / MMETSP_diginorm_streaming_v_not.csv
Created July 12, 2016 19:44
Comparison with transrate of Trinity trascriptome assemblies from 3 MMETSP samples, diginorm streaming vs. not
assembly n_seqs smallest largest n_bases p_contigs_with_CRBB p_refs_with_CRBB reference_coverage
SRR1300409.Trinity.streaming.fixed.fasta_no_orphans 30605 224 4134 19238075 0.97543 0.92568 0.85853
SRR1300409.streaming.fixed.fasta 30457 224 4134 19243907 0.98276 0.93851 0.89009
SRR1300409.Trinity.fixed.fasta 30771 224 4210 19279950 0.98096 0.94858 0.89449
SRR1300402.streaming.fixed.fasta 35128 224 13921 22716553 0.9928 0.98108 0.94234
SRR1300402.not.fixed.fasta 35101 224 13528 22584802 0.99282 0.98024 0.93656
SRR1300410.Trinity.streaming.fixed.fasta 9316 224 4094 5055897 0.99141 0.96962 0.93397
SRR1300410.Trinity.fixed.fasta 9414 224 4096 5077982 0.98959 0.97993 0.94012