Comments (2)
Hi,
The BAM file seems to be valid (cf. #corrupt files: 0
) and ERE also found reads (cf. #reads: 1002408184
). However, no split read was found (cf. #split reads: 0
), which seems to be unrealistic for RNA-seq data.
Read mapper that do not allow split reads (like bwa mem), could produce such a BAM file without split reads leading to such a result. You need to use a read mapper that allows split reads, e.g. TopHat, HISAT2 or STAR .
Does this help?
BTW, you do not need to merge the individual BAM files. You can run ERE with multiple bam files.
best regards, Jens
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Hi, Jens-
I used bwa mem, so this absolutely answers my question!
I tried running ERE with the bam files separately while troubleshooting, so I will continue running this way.
Thank you!!
My best,
Emma
from jstacs.
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