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Kingsford-Group / squid

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
BSD 3-Clause "New" or "Revised" License
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Question: Does Squid work on ISO-seq? #1

Open zeeev opened 7 years ago

zeeev commented 7 years ago

We have ISO-seq alignments using gmap2, Will squid run on these data?

Congm12 commented 7 years ago

The current implementation assumes paired end reads with inward orientation. And that information is used in distinguishing discordant reads with concordant, which affects genome segmentation but not rearrangement. For ISO-seq, the reads setting should be different, and requires a different implement of parsing reads. So short answer is I don't think it will run correctly on ISO-seq now. But I would like to look into ISO-reads alignment, and implement parsing long reads in the future.