I found some 10x single-cell RNA seq data on GEO that I want to use for a study (SRR7754181). Unfortunately, it looks like the author only submitted read2 of the raw fastq files. They did include a bam file but it looks like it is already processed.
I was wondering if there is a way to split this file into fastq read1 and read2 so that I can realign it with cellranger. The study in question used an outdated version of cellranger count. When I try to split with samtools fastq, I get two empty fastq files. Am I missing something obvious?
samtools flagstat /12.5.bam.1 241289956 + 0 in total (QC-passed reads + QC-failed reads) 78389287 + 0 secondary 0 + 0 supplementary 1246988 + 0 duplicates 220870315 + 0 mapped (91.54% : 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) samtools fastq -@ 8 /12.5.bam.1 -1 E12_R1.fastq.gz -2 E12_R2.fastq.gz -0 /dev/null -s /dev/null -n [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 162900669 reads