JialiUMassWengLab

I have the same issue. After installation there's a prompt to update to version 1.0.1 with pip install. After that the VIP panel disappeared. @interactivereport @z5ouyang any suggestions please?

After communicating with the developers, version 1.0.1 is not ready yet. So users should refrain from upgrading to v1.0.1 for now. Additionally it is advisable to use the Scanpy contained...

Hi Chong, This is quite unusual. I've never seen error messages like this and I don't think there's a "getBin" call in the program. Can you provide more details? Jiali...

Hi Tao, I removed the dependency on samtools view -X option. Now TEMP works for newer versions of samtools (1.x) as well. Please let me know if you encounter further...

It's most likely a samtools version issue. I've remove the dependency on samtools view -X option. Now TEMP works for newer versions of samtools (1.x) as well. Please try again...

Hi Rimjhim, It's hard to know exactly what happened without knowing anything about "merged.Ma99.bam". Would you mind posting a few entries (including read "HWI-700523F:21:C6KJ9ANXX:4:2301:14610:90784/2") from the BAM file? Jiali

Rimjhim, This is caused by having very long reads and the two reads actually overlap. I've modified the code and it should be taken care of. Let me know if...

Hi Mike, Thanks for your comments. I'll try to accommodate the "bwa mem" mapping method.

Hey guys, I made the modifications now that TEMP is compatible with BWA mem. I take advantage of two tags in the SAM files outputted by BWA mem: "AS:i:" which...