cDNA reads aligning poorly

[vkkodali]

I have tried to align the cDNA reads using minimap2 but only a small number of reads align to the human genome asn shown in the table below:

comment	count
Total reads in the FASTQ file	24531552
Reads passing filtering	11202168
Reads aligned	1656
Unmapped reads	11200512

I run minimap2 on the filtered set of reads using the following command:

minimap2-2.17_x64-linux/minimap2  \
  -ax splice -t 16 --eqx --MD --cs -G 1300000 -Y  \
  --junc-bed GCF_000001405.39_GRCh38.p13_genomic.bed12 \ 
  GCF_000001405.39_GRCh38.p13_genomic.ont.mmi filtered_fastq.fq.gz -o output_file.sam

I was able to use the same junc-bed and index files with the direct RNA sequencing reads and get good alignments so I do not suspect those two files.

[mitenjain]

This seems odd. We will try to reproduce this issue and resolve it shortly.

Thank you for bringing this to our notice.