Closed francicco closed 4 years ago
Hi @francicco,
Sorry for the delay in getting back to you -- I've been on vacation for the past couple of weeks.
First of all, tigmint expects the barcode to be in the BX:Z
tag of your reads -- it looks like you have your reads formatted how older versions of ARCS required the barcode? If you use the reads output from longranger basic
, then the barcode will be in the tag where it is expected.
In addition, as you suspected, I think the naming of your reads are preventing the aligner from recognizing that they are paired end with -p
. The /1
and /2
suffixes are fine when they are at the end of the read header, but the _<barcode>
addition is interfering. I bet that when you specify the R1/R2 separately, it doesn't have to do the smart pairing logic, thus it works better.
Basically, I think if you use the interleaved output file from longranger basic
with the barcode in the BX:Z
tag, that should solve your issues.
Hope that helps! Lauren
Hi Lauren,
Thanks a lot, I solved this some time ago! :) I hope you enjoyed your vacation. Best, F
Glad to hear you got it sorted out! :)
Hi @lcoombe,
I changed cluster and I had to reinstall the software. Now I'm testing if the new environment works. What I did was to map mu linked reads to the assembly using
bwa mem -t$THREADS -C $ASSEMBLY.fasta -p $READS | samtools sort -@$THREADS -tBX -o $ASSEMBLY.LinkedReads.sortbx.bam
The fist possible problem is that bwa mem doesn't recognise the paired reads, and I think maps them as single endsMy reads headers are like this:
Maybe the
/1
and/2
is the problem.But I also tried:
bwa mem -t$THREADS -C $ASSEMBLY.fasta $READ1 $READ2 | samtools sort -@$THREADS -tBX -o $ASSEMBLY.LinkedReads.sortbx.bam
and the mapping seems fine.After that I execute:
tigmint-molecule $ASSEMBLY.LinkedReads.sortbx.bam | sort -k1,1 -k2,2n -k3,3n
bit everything is silent. What am I doing wrong?