Overall alignment 0.00%

Question

[heeyairenkhaba]

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.

[Carambakaracho]

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.

[ATpoint]

Read length would also be good to know? I guess something like 25bp or so?

[Bastien Hervé]

Same team ? Or is it just a huge concomitance ?

RNA-seq alignment rate is too low.

[heeyairenkhaba]

I downloaded an SRA file of mouse riboseq data. Using this codes SRA toolkit . here is my aignment code.

hisat2 -p 8 -x /path /to /hisat2_index_mus_musculus --dta --rna-strandness F -U /path/to//SRR5908901.fastq -S /path/to output/SRR5908901.sam

Before this I used Cutadapt to trim sequence between 15 -50 nucleotide having Phred value 15

[finswimmer]

Hello and welcome to biostars heeyairenkhaba ,

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Thank you!