Philip Lijnzaad
Philip Lijnzaad
just a comment for those of you (like myself) who would try to use some FIFO magic for this: solving it as something like `atropos -a RA5=GATCGTCGGACTGTAGAACTCTGAAC -se TM433_trunc.bam --input-format...
Hi, I installed bamnostic (version 1.1.4) and it finds it etc. but it still doesn't work. With bamnostic, atropos again crashes on input bam files that contain `@CO` header lines...
Brililant, seems to work fine, many thanks. I realized that I overlooked the fact that leaving out the` -o `option already resulted in output to stdout - sorry! Still puzzled...
Weirdly, converting (to SAM) the original bam and the reformatted (bam->sam->bam) versions are identical. I also did a strict check with ValidateSamFile from picardtools-2.21.1, both bams give identical (and harmless)...
Brilliant, thanks!
This is very nice, but it's a terrible name as it interferes with `/usr/bin/split`, leading to hard-to-trace bugs. Please rename it to `split_string` or somesuch :-)
What's with all the thumb down's ? Please be constructive, folks!
I would be in favour of adding this, but it's not trivial (the `source`d file could itself `source` yet more files in turn). Other than that: kudos to @ersiner for...
out of interest, is there a reason you don't use the --skip_remap option? That avoids wasting a great deal disk space and CPU cycles by not running the full minimap...
Hi Xi, thank you for you quick reply! The large majority of single indexed reads have `GGGGGGGGGG` as the fake second index read. Demultiplexing with this as `Index2` gives yields...