Unmapped reads from STAR
Hello,
I am interested to look at the output of the unmapped reads which I obtained after STAR alignment
Unmapped.out.mate1 Unmapped.out.mate2
and use this to BLAST the unmapped reads against the full NCBI database to see if there are any hits or just rRNA contamination? Could anyone please let me know how to do this with this output?
• 6,462 views
•
link
updated
by
Ram
•
written
by
spaul8505 •
•
written
by
spaul8505 •
1 answer
Convert the unmapped BAMs to fasta (see how here) and blast the fasta.
However, if you have too many unmapped reads, the blast will take forever. A faster alternative would be to download rRNA database, convert the unmapped BAMs to fastq and use FastQ_Screen (or Bowtie / BWA / your preferred mapper directly) to estimate rRNA contamination.
Log in to answer this question.
More posts like this
-
How to construct a blast database for non-green plant species and fungi
written by Sony Nguyen •
-
RNA-seq pipeline
written by Javier •
-
Low mapping percentage
written by Sib •
-
Archeological DNA sample - how to analyze
written by Aruna •
-
how to have aligned region in fasta format using blastn?
written by mthm •
-
Extracting Unmapped Reads from BAM files using Rsamtools
written by dk0319 •
-
Remove contamination before assembly
written by bruseq •
-
output unmapped file in STAR alignment
written by linjc.xmu •
-
STAR Unmapped reads
written by prathyushareddy87 •
-
Saving unmapped reads from STAR
written by mihaell •
