0% Mapped Reads

[reemelkabbout]

Hi Alex,

I ran the following command

STAR-2.7.10a/source/STAR --readFilesCommand gunzip --quantMode TranscriptomeSAM --outFilterMismatchNmax 999 --sjdbGTFfile /home/elkree01/RNAseqAug2022/Homo_sapiens.GRCh38.107.gtf --genomeDir ref/ --outSAMstrandField intronMotif --sjdbScore 1 --alignIntronMin 20 --outSAMattributes NH HI AS NM MD --outSAMunmapped Within --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outSAMtype BAM SortedByCoordinate --alignSJoverhangMin 8 --alignMatesGapMax 1000000 --outFileNamePrefix test_ctrl --outFilterMismatchNoverReadLmax 0.04 --outWigStrand Unstranded --runThreadN 10 --readFilesIn /home/elkree01/RNAseqAug2022/H45_R1.fastq.gz /home/elkree01/RNAseqAug2022/H45_R2.fastq.gz

But I got 0 mapped reads, could you please help me find out where the problem is?

Started job on | Sep 08 11:28:45 Started mapping on | Sep 08 11:38:57 Finished on | Sep 08 11:39:01 Mapping speed, Million of reads per hour | 0.00

                      Number of input reads |   0
                  Average input read length |   0
                                UNIQUE READS:
               Uniquely mapped reads number |   0
                    Uniquely mapped reads % |   0.00%
                      Average mapped length |   0.00
                   Number of splices: Total |   0
        Number of splices: Annotated (sjdb) |   0
                   Number of splices: GT/AG |   0
                   Number of splices: GC/AG |   0
                   Number of splices: AT/AC |   0
           Number of splices: Non-canonical |   0
                  Mismatch rate per base, % |   -nan%
                     Deletion rate per base |   0.00%
                    Deletion average length |   0.00
                    Insertion rate per base |   0.00%
                   Insertion average length |   0.00
                         MULTI-MAPPING READS:
    Number of reads mapped to multiple loci |   0
         % of reads mapped to multiple loci |   0.00%
    Number of reads mapped to too many loci |   0
         % of reads mapped to too many loci |   0.00%
                              UNMAPPED READS:

Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 0 % of reads unmapped: too short | 0.00% Number of reads unmapped: other | 0 % of reads unmapped: other | 0.00% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%

Thank you!

[alexdobin]

Hi @reemelkabbout

please check that gunzip command works: gunzip /home/elkree01/RNAseqAug2022/H45_R1.fastq.gz | head