Entering edit mode
5 months ago
akh22
▴
120
HI,
I have an ATAC bam generated by 10X CellRanger ARC which was further processed to get the read mapped in proper pair as follows;
samtools view -b -f 0X2 -@40 Cellranger_output/sorted.atac.noscafoold.bam > test.bam
Then I run bamCoverage with --MNase option as follows;
bamCoverage -b test.bam \ -bs 1 \ --MNase \
-b blacklist/blacklist.bam \
--effectiveGenomeSize 2913022398 \
--exactScaling \
-e \
-p 20 \
-of "bigwig" \ -o sorted.atac.noscafoold.bam.mod.bigwig
And I run into this error;
*Error*: For the --MNAse function a paired end library is required.
Blacklist.bam was generated as follows;
bedToBam -i ENCFF356LFX.merged.mod.bed -g ../gencode/GRCh38.primary_assembly.genome.fa.fai > test.bam
What am I missing ?
As rfran010 pointed out, I screwed up the script big tme. The right one is as follows;
This run is completed just fine;