Sefi_(Yair)_Prawer comments

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                                            Sefi_(Yair)_Prawer

Explanation of txClassDescriptions and error message for large bam file.

Hi Asher, I am having the same issue with a subset of my files. I had a feeling it had something to do with the size of the bam files....

Explanation of txClassDescriptions and error message for large bam file.

Hi Andre, Thanks for help on this issue, Yes it appears some BAM files generate this error while others do not. The BAMs were all generated using the same minimap...

Explanation of txClassDescriptions and error message for large bam file.

Hi Andre, Yes that does seem very strange. I expect spliced and unspliced reads. This bam file contains ~92M primary alignments I have successful runs with some bam files using...

Explanation of txClassDescriptions and error message for large bam file.

Hi Andre, Yes i agree an example would be useful. I have subset the bam based on a single gene i know is in my data. I have viewed this...

Explanation of txClassDescriptions and error message for large bam file.

Hi Andre, It looks like i have been able to get bambu to run on these problematic bams. As you suggested i filtered the bams to retain only alignments mapped...

Explanation of txClassDescriptions and error message for large bam file.

Hi All, Im back with same error Unfortunately. The input bam file is from a different sample and i have tried removing secondary and supplementary alignments. Mapping was performed to...

Explanation of txClassDescriptions and error message for large bam file.

Hi Andre, Thanks for the suggestion re HongYhong's Fix. This seems to have worked! I am not getting the "reads count for all annotated junctions: 0 (0%)" message probably because...