High intronic mappings in the RNASeq

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5.1 years ago

shangyuan5000 ▴ 30

Hi, I have some samples from a frozen tissue bank, extract the RNA and sent them to RNASeq. The result mappings are weird to me, with 30~40% mapping rate by Salmon. I tried hisat2, the mapping rate goes to >80%. samtools sort the sam files to bam, and them qualimap2 gives me the QC results:

Exonic: | 31,212,828 / 41.39%

Intronic: | 39,191,136 / 51.97%

Intergenic: | 5,008,406 / 6.64%

Intronic/intergenic overlapping exon: | 6,243,753 / 8.28%

There is not too much DNA contamination, but a large portion of intronic mappings. Is there anyone who knows how to interpret this result? What can I do with this RNASeq results?

Any advice is welcome.

Best regards, Raymond

RNA-Seq • 1.8k views

ADD COMMENT • link 5.1 years ago by shangyuan5000 ▴ 30

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Depends on the organism and how well the genome is annotated, as well as whether you used polyA or ribo depletion libraries. So providing more details would be helpful

ADD REPLY • link 5.1 years ago by ashok.ragavendran ▴ 50

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I used human hg38 Ensembl release 84. ribo depletion is used

ADD REPLY • link 5.1 years ago by shangyuan5000 ▴ 30

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This paper suggests ployA method is much better method to use https://www.nature.com/articles/s41598-018-23226-4

Also I'd like to point out that Salmon and HTseq seem to agree. About ~40% of your reads are exonic. How's the coverage across the exonic regions? If they're good then you can continue as normal IMO, that's assuming you performed deep sequencing.