I’m trying to make the .bam file for analysis on NIPTeR. But now the file looks like having some problems I cannot understand. Bin_bam_sample always return “Error in splitted_reads[[2]] : subscript out of bounds.
Here is method that I use:
Remove duplicates with fastp
Bwa aln follow with bwa samse
Convert .sam to .bam and only keep foward strand: samtools view -F 0x10 -bq 20 -S sample.sam.gz > sample.bam.gz
Samtools collate and samtools fixmate after that
Remove duplicate with GATK Picard
p/s: I just found out I need both foward and reverse strand. However, the sequencer is single-ended and so I think I only need foward strand. Is there a way for me to process on NIPTeR by just using .bam file contain foward strand only?
I’m trying to make the .bam file for analysis on NIPTeR. But now the file looks like having some problems I cannot understand. Bin_bam_sample always return “Error in splitted_reads[[2]] : subscript out of bounds.
Here is method that I use:
p/s: I just found out I need both foward and reverse strand. However, the sequencer is single-ended and so I think I only need foward strand. Is there a way for me to process on NIPTeR by just using .bam file contain foward strand only?