Yichao Li

Hello, Is there a good way to visualize these clipped reads? If I visualize the bam file in IGV, since the same read is split into multiple alignments, I can't...

Thank you so much for the quick response! Would you mind explain a bit more about the 6kb receptive field? Number of layers should not affect. Do you mean number...

I added a linux version: https://anaconda.org/liyc1989/dna_features_viewer If there's any copyright issue, please let me know, I will delete it. Thanks, Yichao

BTW, I think crispresso can take bam as input, instead of fastq, but looking at the code, I think what the program really does is extracting the reads from the...

Thanks for the quick reply! I don't have a very challenging dataset, I can just solve my problems by some data cleaning. Looking forward to this FLASH-less version! Thanks, Yichao

For the 34bp dsODN sequence, we use a score cutoff of 30, which could potentially allow up to 7 mismatches or a short gap. for `StripedSmithWaterman`, a match is +2...

New to velocity analysis. Thanks for this note! I'm wondering, in terms of the correctness, should we use the raw counts or some normalized values for `RunVelocity()`? Thanks, Yichao

same problem here

having the same problem here

Hi @[fairliereese](https://github.com/fairliereese), can you provide more details on how to use `lapa`? It seems that we should use `lapa_correct_talon` instead of `lapa`? Thanks, Yichao