Current TraCeR script expects existence of $sample_$region_{1,2}.fastq in order to resume from bowtie2 output. With single end data, _{1,2} are never appended and so read alignment is never resumed from. This is just a simple fix adding a conditional on single_end value.
mstubb
commented
8 years ago
Current TraCeR script expects existence of
$sample_$region_{1,2}.fastqin order to resume frombowtie2output. With single end data,_{1,2}are never appended and so read alignment is never resumed from. This is just a simple fix adding a conditional onsingle_endvalue.