I am using to align RNA sequence reads to the reference genome I created using STAR. I have done the QC of every fastq file before running the mapping job. The problem I am encountering is that some of the fastq files are generating empty BAM files, whereas, other files have no problem. I am hereby attaching Log.final.out files. The first one is for the file for which I had no problem:
more Log.final.out2 Started job on | May 14 16:55:48 Started mapping on | May 14 16:59:56 Finished on | May 14 17:06:24 Mapping speed, Million of reads per hour | 97.45
Number of input reads | 10503242
Average input read length | 66
UNIQUE READS:
Uniquely mapped reads number | 6887932
Uniquely mapped reads % | 65.58%
Average mapped length | 65.33
Number of splices: Total | 471329
Number of splices: Annotated (sjdb) | 460539
Number of splices: GT/AG | 462632
Number of splices: GC/AG | 3610
Number of splices: AT/AC | 302
Number of splices: Non-canonical | 4785
Mismatch rate per base, % | 0.49%
Deletion rate per base | 0.01%
Deletion average length | 1.93
Insertion rate per base | 0.02%
Insertion average length | 1.83
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 2756203
% of reads mapped to multiple loci | 26.24%
Number of reads mapped to too many loci | 38499
% of reads mapped to too many loci | 0.37%
UNMAPPED READS:
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 7.23%
% of reads unmapped: other | 0.58%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
The second Log.final.out file looks like the following: more Log.final.out Started job on | May 14 17:25:16 Started mapping on | May 14 17:33:08 Finished on | May 14 17:33:10 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:
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 0.00%
% of reads unmapped: other | 0.00%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
I have not modified the command for the above two jobs (apart from the fact that these files are in different directories ). Here is the generic command: STAR --genomeDir /users/PFS0231/cls0226/Createindex2/ --runThreadN 1 --readFilesIn /users/PFS0231/cls0226/output/ALzt14-1/232/ file.fastq --outSAMtype BAM Unsorted
I am so perplexed why am I having this problem. Any help is really appreciated.
Thanks
