In step 4 it says: python src/best_align.py --bam1 1.sorted.bam --bam2 2.sorted.bam --fastq fastq
by --fastq fastq, do you mean the original readout from nanopore, previously called "1d_pass.fq.gz" or something else?
I always get the error: sambamba-pileup: Unexpected 'f' when converting from type string to type long
Has anybody experienced the same error?
The only way I found to solve it was to omit the "-L cpg_sites.bed" which is no final working solution.
Which cpg_sites.bed file did you use?
Hi, thank you for the very useful tool!
I have to questions:
In step 4 it says: python src/best_align.py --bam1 1.sorted.bam --bam2 2.sorted.bam --fastq fastq by --fastq fastq, do you mean the original readout from nanopore, previously called "1d_pass.fq.gz" or something else?
In step 5 $ sambamba mpileup output_CT.sorted.bam -L cpg_sites.bed -o pileup_CT.tsv -t 6 --samtools -f hg19.fa
I always get the error: sambamba-pileup: Unexpected 'f' when converting from type string to type long Has anybody experienced the same error? The only way I found to solve it was to omit the "-L cpg_sites.bed" which is no final working solution. Which cpg_sites.bed file did you use?
I appreciate any suggestions, kind regards