Hello,
I am using ASPli for a dataset with 94 FASTQ files (scRNA-Seq with Smart-Seq2 full transcript). I used STAR for alignment and build all required dataset based on the same genome version.
What might be the problem. Minimum read length in my BAM files is 28 so I used it, chromosome notations are same with GTF and Fasta file. I used ASPli before but it never happened.
Hello, I am using ASPli for a dataset with 94 FASTQ files (scRNA-Seq with Smart-Seq2 full transcript). I used STAR for alignment and build all required dataset based on the same genome version.
When I run gbCounts with this code,
gbcounts <- gbCounts(features=features, targets=targets, minReadLength = 28, maxISize = 50000 , libType = "SE")gbcounts@junction.counts section is full of zeros and looks like this:
junction gene strand multipleHit symbol gene_coordinates bin_spanned j_within_bin 1.90050.90287 noHit noHit - - - - - 1.91629.92091 noHit noHit - - - - - 1.120869.120874 noHit noHit - - - - - 1.155831.164263 noHit noHit - - - - - 1.180569.180902 noHit noHit - - - - - 1.185350.185491 noHit noHit - - - - - 1.268204.268667 noHit noHit - - - - - 1.357586.358049 noHit noHit - - - - - 1.378590.380475 noHit noHit * - - - - -
What might be the problem. Minimum read length in my BAM files is 28 so I used it, chromosome notations are same with GTF and Fasta file. I used ASPli before but it never happened.
Thank you in advance.