I just did the alignment of my samples and for one of the samples, STAR used only 1% of the reads of the trimmed fastq file for mapping. Does someone know, what the reason could be for that? The references I used worked just fine for the rest of the data and I ran out of ideas where the error lies.
The FASTQ file contains around 300 million reads and STAR only uses 3 million. This is the command I used (its the last alignment step of a 2 pass run):
STAR --outFilterType BySJout --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.04 --alignEndsType EndToEnd -runThreadN 8 --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 4 --alignIntronMax 300000 --alignSJoverhangMin 8 --alignIntronMin 20 --genomeDir /path/to/Genome/ --sjdbOverhang 149 --quantMode GeneCounts --sjdbGTFfile /path/to/hg91.gtf --readFilesIn /path/to/file.fq > STAR.log
This is the Final log of the STAR run:
Started job on | May 14 16:56:28 Started mapping on | May 14 16:59:07 Finished on | May 14 17:02:06 Mapping speed, Million of reads per hour | 65.72 Number of input reads | 3267930 Average input read length | 134 UNIQUE READS: Uniquely mapped reads number | 3111505 Uniquely mapped reads % | 95.21% Average mapped length | 135.04 Number of splices: Total | 1497184 Number of splices: Annotated (sjdb) | 1497124 Number of splices: GT/AG | 1483304 Number of splices: GC/AG | 12329 Number of splices: AT/AC | 1093 Number of splices: Non-canonical | 458 Mismatch rate per base, % | 0.18% Deletion rate per base | 0.01% Deletion average length | 1.85 Insertion rate per base | 0.01% Insertion average length | 1.51 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 116052 % of reads mapped to multiple loci | 3.55% Number of reads mapped to too many loci | 492 % of reads mapped to too many loci | 0.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.75% % of reads unmapped: too short | 0.41% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
Any help is greatfully appriciated!