bowtie no reported alignment?

Question

[bxia]

bowtie no reported alignment? I used the same command before, but this time.. there is no reported alignment..

Anyone have the same situation before??

[mks002]

The first question is did u changed the reference this time?

One thing might be that there is contamination in the sample. So take some random 1000 reads and do an online blast.

The blast output will show what organism is there in the sample and then you can cross check that what reference you have selected is correct or not.

Below are the simple steps u can follow

seqtk sample -s100 Input.fq 1000 > Output.fq

Then Convert a FASTQ file to FASTA and do a online blast:

sed -n '1~4s/^@/>/p;2~4p' Output.fq > Output.fa

Try it might be helpful.

[bxia]

Thanks for your reply, it turns out to be a server error.

Thanks again