Error after STAR mapping

Question

[potter]

Hi, I’m doing the STAR mapping, but I get the bam files with some problems.When I use the command samtools flagstat SRR7195620_2.fastq.gz_Aligned.sortedByCoord.out.bam to see the details of the bam file,it shows this:

3266075 + 0 in total (QC-passed reads + QC-failed reads)
1044500 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
3266075 + 0 mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

My command to build STAR index is

STAR --runThreadN 20 --runMode  genomeGenerate --genomeDir  ~/home/STAR_human_index/1 \--genomeFastaFiles  ~/referenceGenomes/FASTA/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile ~/referenceGenomes/GTF/Homo_sapiens.GRCh38.98.gtf \--sjdbOverhang 109

And my command to do STAR mapping is

ls -d SRR*|while read SRR; do echo $SRR; STAR --runThreadN 20 --genomeDir ~/home/STAR_human_index/1 --readFilesCommand gunzip -c --readFilesIn ~/home/fastq/${SRR} --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outFileNamePrefix ~/BAM_results/bamtest/${SRR}_; done

I don’t know where the problem is,can anyone do me a favor?Thanks a lot!

[GenoMax]

but I get the bam files with some problems

What kind of problems? Result above shows that 100% of your input reads have mapped. Is the number of reads not same as expected? You have a lot of secondary alignments.

[potter]

Thank you for your reply! But I don’t know the meaning of

0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped

Because when I use this file in rMATS4.0.1,the result only has title, and the content is blank.While using the sample bam file of rMATS 4.0.1,I can get results. I see the sample bam files in samtools flagstat command,and the result is

47978 + 0 in total (QC-passed reads + QC-failed reads) 5088 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 47978 + 0 mapped (100.00% : N/A) 42890 + 0 paired in sequencing 21445 + 0 read1 21445 + 0 read2 42890 + 0 properly paired (100.00% : N/A) 42890 + 0 with itself and mate mapped 0 + 0 singletons (0.00% : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)

So I wonder if the difference between this is the reason? By the way,the rMATS shows my own bamfile input 0 reads .Thanks for your help!

[swbarnes2]

Having no paired results is appropriate when you only have a single fastq file as input.