User: hsu

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hsu0
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Posts by hsu

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perl compilation errors
... I want to extract fpkm information and I used a perl script: more PB_stressed_sample.txt | perl -ne 'BEGIN{my %F;my %G; my $C=0; @S=("gene","genename");}@a=split;push @S,$a[0];open(my $fh, "<", " SRX3084$a[0]/genes.fpkm_tracking");$C++;<$fh>;while (my $row = <$fh>) {@b=spli ...
assembly written 5 days ago by hsu0 • updated 5 days ago by Michael Dondrup44k
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Comment: C: featureCounts problem annotation
... Thank you very much ...
written 6 days ago by hsu0
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Comment: C: featureCounts problem annotation
... I got these two files `genecounts_888 genecounts_888.summary` without `-t gene` Is this correct ? ...
written 6 days ago by hsu0
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Comment: C: featureCounts problem annotation
... I ensembl start_codon 538 540 . + 0 exon_number "1"; gene_biotype "protein_coding"; gene_id "YAL068W-A"; gene_name "YAL068W-A"; gene_source "ensembl"; gene_version "1"; p_id "P5379"; transcript_biotype "protein_coding"; transcript_id "YAL068W-A"; transcript_so ...
written 6 days ago by hsu0 • updated 6 days ago by genomax51k
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featureCounts problem annotation
... I have download Saccharomyces cerevisiae (Yeast) genome and annotation from Ensembl R64-1-1. code as: featureCounts ./Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Archives/archive-2015-07-17-14-36-40/Genes/genes.gtf -o genecounts_888 -t gene -p -g Name .exprnasamout/SRX3084888.bam Ther ...
genome written 6 days ago by hsu0 • updated 6 days ago by michael.ante2.5k
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Comment: C: Hisat2 build index error
... ok, thank you. I re-download the reference genome several times. But still the same error. wuwuwu.... ...
written 7 days ago by hsu0
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Comment: C: Hisat2 build index error
... These are two commands outputs: S288C_reference_genome_R64-2-1_20150113/0000775000554500003120000000000012463257272016120 5ustar shuaishuaiS288C_reference_genome_R64-2-1_20150113/rna_coding_R64-2-1_20150113.fasta0000664000554500003120000054452712455312025023155 0ustar shuaishuai>HRA1 ...
written 7 days ago by hsu0
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Comment: C: Hisat2 build index error
... There aren't the two commands print that you asked. ...
written 7 days ago by hsu0
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Comment: C: Hisat2 build index error
... Settings: Output files: "./INDEX.*.ht2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence leng ...
written 7 days ago by hsu0 • updated 7 days ago by genomax51k
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Comment: C: Hisat2 build index error
... still the same error ...
written 7 days ago by hsu0

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