mega_from_bams.sh not working

[Pavla Navratilova]

When running mega_from_bams.sh using .bam files created by other than juicer toolkit (HiCUP here), the $splitdir in the script is not specified and is not available for generating inter.txt and further.

also

samtools view "$cThreadString" -F 1024 -O sam "${outputDir}"/mega_merged_dedup.bam | awk -v mapq=1 -f "${juiceDir}"/scripts/common/sam_to_pre.awk > "${outputDir}"/merged1.txt

........runs but produces an empty file, while the piped output seems fine:

samtools view -@30 -F 1024 -O sam mega_merged_dedup.bam | head A00703:39:HTKMFDRXX:1:1101:14326:1031 99 chr4H 434501938 35 151M chr6H 447625737 0 AGACAGAAGCTTTCGGCGACGGAAAAGTACTTTCGATGATATCCTGATTTTTTGTGGAATTTTTGGGGATATATAGGCGCAAACCCTAGGGCAAAGGAGGTCTAGGGGGCCCACAAGCCTGTGGGCCGCGGCCTCCCCCTGTCCATGGGGT FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF::FFF::FFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-50 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:151 YT:Z:UU CT:Z:TRANS A00703:21:HMMYTDMXX:1:1101:31349:1047 99 chr6H 60241394 35 151M = 60241514 0 ACATATCTCTCTGTGTTATAACTGTTGCATGATGAATAGCATCCGGCATAATCATCCATCACCGATCCAATGCCTATGAGTCTTTCCTACTGGTCCTTGCTACATTACTTTGCCGCTACTGCTGTCACTGCTGCTACTATTACTTTGACGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFF AS:i:0 XS:i:-47 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:151 YT:Z:UU CT:Z:CLOSE A00703:21:HMMYTDMXX:1:1101:31349:1047 147 chr6H 60241514 38 150M = 60241394 0 GCTGTCACTGCTGCTACTATTACTTTGACGGTAGTGTTGTTACTTTGCTGCTACTAGTTACTGTTGCTACTGCTGCTATCATACTACCTTGCTACTGATACTTTGCTGCACATACTATATCTTTCAGATGTGGTTGAATTGACAATTCAA FFF,F,FFFFF:FFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FF:FFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-76 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:150 YT:Z:UU CT:Z:CLOSE .......

[Muhammad Shamim]

A couple options:

1 - Use Juicer 1.6 (from Github releases) and follow the advice here: 

https://groups.google.com/g/3d-genomics/c/c5F31sGQeAg/m/P3b31apUAQAJ

2 - Reprocess the experiments with Juicer starting with the raw fastqs

The HiCUP developers or someone in the community who has used HiCUP may have more suggestions.