Comments (4)
I am not familiar with pysam. Please redo alignment for these few reads and output in the PAF format.
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I have found my mistake after outputting alignments in the PAF format.
I forgot to recalculate the coordinates when the reads are reversely mapped. Sorry for taking up your time.
Best,
Xiaofei
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No problem. Thanks for the confirmation. Falign is also a capable tool for aligning pore-C reads. It doesn't generate any overlaps between fragments. You may consider to give it a try as well.
from minimap2.
Thank you for you suggestion, I'm also trying out that tool.
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Related Issues (20)
- Mapping of post-polyA region HOT 4
- Why -Y parameter makes bam size pretty larger HOT 1
- radix_sort_128x() produces unstable sorting output
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- minimap2 crashes w/o informative debugging information HOT 1
- ONT cDNA reads with polyA were not aligned to reference HOT 1
- Question about parameter -uf HOT 2
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- [mappy] DP alignment score in Alignment objects
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- unrecognized type ':' from alignment tags HOT 1
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- Minimap2 truncating the alignments if there is a SNP at the start of the gene HOT 1
- minimap2 misses alignment of sequence to reference HOT 1
- force full query alignment
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