I get the error "chromosome in SAM file not found in reference:chr1 "when running methcounts command "methcounts -c /methpipe_reference/mm27 -o 1979.meth 1979.mr.sorted_start"
I am using methpipe v4.1.2 alpha.
The mr file was generated by converting the deduplicated bam file from bismark to sam using samtools; then converted to mr using format_reads and subsequently sorted to sorted_start.
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I get the error "chromosome in SAM file not found in reference:chr1 "when running methcounts command "methcounts -c /methpipe_reference/mm27 -o 1979.meth 1979.mr.sorted_start"
I am using methpipe v4.1.2 alpha.
The mr file was generated by converting the deduplicated bam file from bismark to sam using samtools; then converted to mr using format_reads and subsequently sorted to sorted_start.