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Difficulty mapping Ribo-seq reads to annotated transcriptome features
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2.1 years ago
jpcchoy • 0

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 and am running out of ideas.

What I've done so far, briefly: retrieved FASTQ, trimmed reads, filtered out rRNA, prepared RSEM reference, calculated expression with RSEM, sorted BAM, used htseq-count on BAM and Gencode GFF3/GTF.
Htseq-count says all reads map to 0 features.

A little more detail:
1. Retrieved SRR FASTQ from SRA using fastq-dump.
2. PolyA adapters trimmed, with cutadapt (new file: same # of reads, now variable length, 25-40 bases).
3. Built Bowtie2 index for each of 4 rRNA sequences.
       [28S:NR_003287.2, 18S:NR_003286.2, 5.8S:NR_003285.2, 5S:NR_023363.1]
4. Removed rRNA from FASTQ by Bowtie2 alignment (new file: fewer reads; no rRNA contamination according to fastqc).
5. Used rsem-prepare-reference on gencode.v30.transcripts.fa (retrieved from top of Fasta files section at
6. Used rsem-calculate-expression on the FASTQ reads with the RSEM reference prepared above (outputs multiple files, one of which is a BAM).
7. Sorted the BAM with samtools sort.
8. Used htseq-count on the sorted BAM produced above and gencode.v30.annotation.gff3 (retrieved from top of GTF/GFF3 files section at (Also tried with the GTF file.)
9. htseq returned a column of ENSG codes (which I don't quite understand) and a column of integer values (all 0). At the bottom of the output, it gave the following summary:
__no_feature 1993081
__ambiguous 0
__too_low_aQual 31427753
__not_aligned 2662011
__alignment_not_unique 0

Thanks so much for any help!

Annotation Alignment HTSeq Ribo-Seq RNA-Seq • 686 views
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And I can provide more details if helpful!


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