Mapping using STAR and Bowtie

[boro2014]

Hi all,

I want to perform an alignment of short reads against a reference genome (human genome from Ensembl). For that I've used STAR, and Bowtie (not Bowtie2). I've some questions about that.

1- I've used STAR by setting the more important parameters as follows:

--outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMatchNmin 15

Here is the final log file content generated by STAR:

Number of input reads | 5845995
Average input read length | 27
UNIQUE READS:
Uniquely mapped reads number | 446299
Uniquely mapped reads % | 7.63%
Average mapped length | 25.10
Number of splices: Total | 4043
Number of splices: Annotated (sjdb) | 622
Number of splices: GT/AG | 3930
Number of splices: GC/AG | 108
Number of splices: AT/AC | 5
Number of splices: Non-canonical | 0
Mismatch rate per base, % | 1.74%
Deletion rate per base | 0.08%
Deletion average length | 1.36
Insertion rate per base | 0.04%
Insertion average length | 1.07
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 4346149
% of reads mapped to multiple loci | 74.34%
Number of reads mapped to too many loci | 963965
% of reads mapped to too many loci | 16.49%
UNMAPPED READS:
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 0.31%
% of reads unmapped: other | 1.22%
CHIMERIC READS:
Number of chimeric reads | 1503
% of chimeric reads | 0.03%

According to this, I got a very low rate of uniquely mapped reads (I used the parameter --outFilterMultimapNmax 10).

How can I improve the uniquely mapped reads rate ?

2 - I've also used Bowtie to map the same sample to the same reference genome. Bowtie didn't output the number of uniquely mapped reads and the number of multimapped reads as STAR did. I checked the log file generated by Bowtie:

# reads processed: 5845995
# reads with at least one reported alignment: 4206928 (71.96%)
# reads that failed to align: 1639067 (28.04%)
Reported 98304317 alignments to 1 output stream(s)

I want to output the number of uniquely mapped reads and multimapped reads from the sam file generated by bowtie. So I have done the following:

samtools view -Sb myfile.sam > myfile.bam
samtools view -F 4 myfile.bam | grep -v "XS:" | wc -l

But it didn't work for me, and I got a wrong number of uniquely mapped reads. I know that those commands work for files generated by bowtie2.

Do you have any solution able to retrieve the number of uniquely mapped, and multimapped reads from the sam file generated by bowtie ?

Thanks a lot

[GenoMax]

Cross-posted: https://www.biostars.org/p/309209/