User: jpcchoy

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Posts by jpcchoy

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Comment: C: Finding Ribo-seq reads in annotated UTRs
... Context: Process BAM file rsemout.transcript.sorted.bam... Single-end reads are included. Assign alignments to features... Segmentation fault (core dumped) ...
written 1 day ago by jpcchoy0
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Comment: C: Finding Ribo-seq reads in annotated UTRs
... I just tried this a few times with different parameters, and every time I get a Segmentation fault (core dumped) Do you know why this might be? ...
written 1 day ago by jpcchoy0
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Comment: C: Finding Ribo-seq reads in annotated UTRs
... Yes! I had not noticed that h.mon, but you're absolutely right. Unfortunately, I've run htseq-count in the following way and all of my sequences map to 0 features... htseq-count -f bam -r pos sorted.bam gencode.v30.annotation.gtf All I get is this: __no_feature 1993081 __ambiguous 0 ...
written 2 days ago by jpcchoy0
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Comment: C: Finding Ribo-seq reads in annotated UTRs
... And I can provide more details if helpful! ...
written 3 days ago by jpcchoy0
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Comment: C: Difficulty mapping Ribo-seq reads to annotated transcriptome features
... And I can provide more details if helpful! ...
written 3 days ago by jpcchoy0
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Difficulty mapping Ribo-seq reads to annotated transcriptome features
... Hi, everyone. I recently tried to map Ribo-seq reads to annotated portions of the transcriptome using **htseq-count**, and everyone of my sequences mapped to 0 features. I don't know what's going wrong! Any help would be **hugely** appreciated! I have been struggling with this for a couple of days ...
htseq annotation alignment rna-seq ribo-seq written 3 days ago by jpcchoy0
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Finding Ribo-seq reads in annotated UTRs
... Hi, everyone. I would like to work out which of my Ribo-seq reads map to UTRs, but haven't been able to find any annotation files (GTF/GFF3) including UTRs or ORFs. I was hoping to align my FASTQ reads against a Gencode.v30 reference, then take the SAM file and use **htseq-count** on it with a Ge ...
htseq ribo-seq utr alignment annotation written 3 days ago by jpcchoy0

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