User: bkinzep

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bkinzep0
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Posts by bkinzep

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Comment: C: HTSeq & featureCounts show no features
... It looks like using the Scaffold FASTA file worked (with the original GFF)! Thank you everyone for your help, it is greatly appreciated! ...
written 11 months ago by bkinzep0
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Comment: C: HTSeq & featureCounts show no features
... These are the headers on the genomic fasta file: >fig|6666666.35312.peg.1 >fig|6666666.35312.peg.2 >fig|6666666.35312.peg.3 I am specifically telling HTSeq count to read the ID, which as above in the GFF says ID=fig|6666666.35312.peg.1 So why would it be looking for Scaffold-0? I made the ...
written 11 months ago by bkinzep0
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Comment: C: HTSeq & featureCounts show no features
... I intended to map RNAseq data to the genome. I see multiple reads mapping to each gene... is this incorrect? I don't think I understand your comment, sorry. ...
written 11 months ago by bkinzep0
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Comment: C: HTSeq & featureCounts show no features
... Yes the post is updated with the corresponding GTF file for the Bowtie alignment shown. ...
written 11 months ago by bkinzep0
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Comment: C: HTSeq & featureCounts show no features
... Thanks, that is what is was starting to suspect. The "GTF" file was downloaded from RAST under the "GTF" option so I suspect this is an issue with RAST. Is there a good way to generate a GTF file that will be compatible with HTSeq-count? Re-annotation is fine if it will result in a better GTF file ( ...
written 11 months ago by bkinzep0
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HTSeq & featureCounts show no features
... Hi - I am trying to use HTSeq (or even featureCounts) to generate counts for RNAseq data. The data set is from a bacteria (Illumina HiSeq PE). It was mapped to the reference genome with Bowtie - and all looks good. When I try to run HTSeq all the mapped reads are designated as "no feature". Below ar ...
htseq alignment featurecounts rna-seq written 11 months ago by bkinzep0 • updated 11 months ago by h.mon29k

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