For our Ribo-seq data set I tried the star aligner but was able to map only a very small fraction of the reads (<1% in some samples), while most of the reads a discarded for being too short.
What does it means for STAR? Where can I manage the minimum read length?
The ribo-seq data was first trimmed using cutadapt based on the Truseq adapter sequence. I than mapped it to the rRNA and kept only the unmapped reads to be later mapped against the transcriptome using STAR.
How can I increase the number of mapped reads?
$ cat GSM3152885/GSM3152885.Log.final.out Started job on | Jan 19 15:04:37 Started mapping on | Jan 19 15:04:39 Finished on | Jan 19 15:08:50 Mapping speed, Million of reads per hour | 393.02 Number of input reads | 27402469 Average input read length | 40 UNIQUE READS: Uniquely mapped reads number | 173659 Uniquely mapped reads % | 0.63% Average mapped length | 28.52 Number of splices: Total | 501 Number of splices: Annotated (sjdb) | 0 Number of splices: GT/AG | 500 Number of splices: GC/AG | 0 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 1 Mismatch rate per base, % | 2.79% Deletion rate per base | 0.00% Deletion average length | 1.12 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 281767 % of reads mapped to multiple loci | 1.03% Number of reads mapped to too many loci | 12974 % of reads mapped to too many loci | 0.05% UNMAPPED READS: Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 26934058 % of reads unmapped: too short | 98.29% Number of reads unmapped: other | 11 % of reads unmapped: other | 0.00% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
Looks like the reads length is 40 bp. Have you tried ungapped mapping e.g.