I'm running the Dropseq pipeline on a de-novo assembled diatom with gene calls from Maker. The pipeline suggests using STAR-aligner for the read mapping. The only problem is that I'm getting a REALLY low mapping.
Does anybody know if there are parameters I can adjust for this particular dataset in
STAR or another aligner designed to specifically address these types of issues?
Here is my command:
STAR --genomeDir star_index_extended --readFilesIn unaligned_mc_tagged_polyA_filtered.fastq --outFileNamePrefix star_ --runThreadN 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 50 --outReadsUnmapped Fastx
Here is the summary output:
bash-4.1$ cat star_Log.final.out Started job on | May 10 14:58:11 Started mapping on | May 10 14:58:16 Finished on | May 10 20:57:36 Mapping speed, Million of reads per hour | 85.18 Number of input reads | 510139798 Average input read length | 57 UNIQUE READS: Uniquely mapped reads number | 9914109 Uniquely mapped reads % | 1.94% Average mapped length | 58.89 Number of splices: Total | 689950 Number of splices: Annotated (sjdb) | 0 Number of splices: GT/AG | 415996 Number of splices: GC/AG | 11503 Number of splices: AT/AC | 297 Number of splices: Non-canonical | 262154 Mismatch rate per base, % | 4.32% Deletion rate per base | 0.07% Deletion average length | 1.54 Insertion rate per base | 0.03% Insertion average length | 1.64 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 11525318 % of reads mapped to multiple loci | 2.26% Number of reads mapped to too many loci | 11342282 % of reads mapped to too many loci | 2.22% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 84.30% % of reads unmapped: other | 9.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%