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5.5 years ago
skevalkumar
•
0
I am trying to map query sequence with RNA-Seq data. I have tried with BWA-MEM and HISAT2 that gives many reads. However, it does not provide any read with 100% match with query read. I appreciate recommendations in terms of software and parameters.
Let me try to put it a slightly different way and you can confirm is this is correct.
You have RNAseq data i.e. your query(ies). When you try to align those reads (presumably to a reference genome or transcriptome) you are not able to get any alignment?
No, I have my query sequence (around 4kb) and trying to align with one of my RNA-Seq data. When I am getting reads, there is not a 100% match of my read with my query sequence.
You should do these alignments the other way. Use your RNAseq data as the query against your reference (4 kb) and see what happens.
As in less than 100% align or none of the reads align perfectly?
Have you eyeballed your RNASeq data? Isn't your 4kb sequence far longer than any of your reads? How can you expect them to match the query 100% along its whole length like that?
None of the reads aligned perfectly with query sequence
Try doing the mapping by flipping your search. Use the 4kb sequence as reference when you search with your reads.