All Questions
3 questions
5
votes
2
answers
1k
views
Reads mapped to exonic, intronic and intergenic regions
After the alignment step I checked the rnaseq metrics of all the samples. Among 40 samples three samples show high percentage of reads mapped to intronic regions. What could be the reason?
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- 1,272
3
votes
1
answer
3k
views
Strange per sequence GC content results
I would be grateful if someone could take a quick look at these FASTQC results. This is rna-seq paired-end data. From the FASTQC manual, an unusual distribution seems to be suggestive of contamination ...
- 631
1
vote
1
answer
584
views
Alignment QC differences between HISAT2 and Qualimap
I used hisat2 for aligning reads to to the genome. I have an alignment summary for sample1 as follows:
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- 631