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Seongwoo Han ▴ 10
@6d55f695
Last seen 20 days ago
United States

Hello, I am running BAMBU with my datasets. It looks like the error is saying the reference annotation isn't correct, but I used these three files in other long read packages and worked well. Is there anything I missed in the command line? I tried moving the files into the directory too, but it fails with the same reasons. I converted fastq file to sam file using minimap2, sam file into bam file using samtools. I am using cDNA!

I used these command lines to convert fastq file to bam file.

./minimap2 -t 8 -ax splice /home/seong/R/x86_64-pc-linux-gnu-library/4.1/bambu/extdata/hg38.fa /data/long_read/ENCBS944CBA/ENCFF263YFG.fastq -o /data/long_read/ENCBS944CBA/ENCFF263YFG.sam

samtools view -@ 8 -Sb -o /data/long_read/ENCBS944CBA/ENCFF563QZR.bam /data/long_read/ENCBS944CBA/ENCFF563QZR.sam

BAMBU bambu • 155 views
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Andre ▴ 20
@c3f05232
Last seen 5 weeks ago
Singapore

Hi Seongwoo,

I think I addressed this on the Github Issue, but for the sake of users that might find this issue here, I will copy how it was resolved here.

The main issue was due to minimap2 mapping. cDNA and direct RNA samples require different command lines for minimap2. Changing the command line to use the correct method of minimap2 solves the issue.