Overall alignment 0.00%
hi everyone,
I have done alignment using HiSAT2 the result comes likes this
19887884 (100.00%) were unpaired; of these:
19887828 (100.00%) aligned 0 times
36 (0.00%) aligned exactly 1 time
20 (0.00%) aligned >1 times
0.00% overall alignment rate
so I got stuck here.
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heeyairenkhaba •
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What genome do you align against? Where does your data come from? What was your command? Does your reference genome match your data? What is your question?
So I got stuck here.
Read length would also be good to know? I guess something like 25bp or so?
Same team ? Or is it just a huge concomitance ?
RNA-seq alignment rate is too low.
I downloaded an SRA file of mouse riboseq data. Using this codes SRA toolkit . here is my aignment code.
Before this I used Cutadapt to trim sequence between 15 -50 nucleotide having Phred value 15
Hello and welcome to biostars heeyairenkhaba ,
codeoption) to present your post better. I've done it for you this time.ADD REPLYButton below a post you want to reply to.Thank you!