GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1
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Header not contain PG line and duplicate SQ line #20
Hello
I have tried to align with command ./graphmap2/bin/Linux-x64/graphmap2 align -r ref/ecoliref.fa --gtf ref/ecoliref.gtf -d tex1/tex/call_pass/newbasecalltest/high_tex_chop_trim.fastq -o tex1/tex/call_pass/newbasecalltest/quality_graph.sam
Then I need to convert it into a bam file but it showed an error that the PG line is duplicate and also PG line is missing so I cannot convert them.
Both references were downloaded from ensembl.
Any suggestion to solve this?
Here is a screenshot from sam file output
Thanks in advance.
Hello I have tried to align with command
Thanks in advance.
./graphmap2/bin/Linux-x64/graphmap2 align -r ref/ecoliref.fa --gtf ref/ecoliref.gtf -d tex1/tex/call_pass/newbasecalltest/high_tex_chop_trim.fastq -o tex1/tex/call_pass/newbasecalltest/quality_graph.samThen I need to convert it into a bam file but it showed an error that the PG line is duplicate and also PG line is missing so I cannot convert them. Both references were downloaded from ensembl. Any suggestion to solve this? Here is a screenshot from sam file output