Zero Mapping rate

Question

[waqaskhokhar999]

Hi,

I have 150 bp long paired-end virus sequencing (fastq) data, I have performed the QC analysis (Fastqc), trimmed out the bad quality reads (Trim_galore) and mapped the reads against the virus genome using Bowtie2 on default parameters but I have got 0 mapping rate, I am not sure if its actually like this or if I am doing something wrong. The mapping stats are:

10816781 reads; of these:   10816781 (100.00%) were paired; of these:
10816781 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
10816781 pairs aligned concordantly 0 times; of these:
  0 (0.00%) aligned discordantly 1 time
----
10816781 pairs aligned 0 times concordantly or discordantly; of these:
  21633562 mates make up the pairs; of these:
    21633553 (100.00%) aligned 0 times
    9 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate

Any suggestions will be highly appreciated.

[colindaven]

What are you mapping to ? Try mapping to host cell + virus, eg human genome + virus genome (just use cat a b > human_plus_virus.fasta ), rather than just the virus. It could be thereare no viral reads in your sample.

[Trivas]

To add to @colindaven's post, can you share your exact bowtie2 command? I've typically allowed mismatches with bowtie2 and if this is RNA-seq, you should be using a splice-aware software instead of Bowtie2.

Answer 1

[Istvan Albert]

take some of your sequences, and blast them against the representative viral sequences, that way you may get a better understanding what you have.

viral sequences can be notoriously variable even within the same genus, it is possible that nothing maps using bowtie2 default parameters as those are a bit more restrictive than say bwa default parameters

and as colindaven mentions, the host genome may dominate