gevro

require-single-strand-agreement on BAM that contains both duplex and single-strand consensus reads

1

Hi, Is it ok to use the require-single-strand-agreement option in FilterConsensusReads on BAM files that contain both duplex and single-strand consensus reads? i.e. BAM files created by running CallDuplexConsensusReads with...

Missed call - not clear why

11

Hi, We did RNA-seq on a sample on which we know there is a very clear and strong splicing defect, as a positive control for the DROP pipeline. The exon...

Hi, There's wrong info in mapping.xml: 102-186-000 is Sequencing kit 2.0 not 3.0.

Number of samples in outlier analysis

1

Hello, Is there a recommended number of samples for outlier analysis? Thanks

Encoding ASCII up to 255

33

How do I use BString / BStringSet for values > 127? PacBio data uses 0:255 ranges for fp/rp/fi/ri tags. I am trying to use BioStrings to work with these tags....

Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'raw'

30

Hi, I'm encountering a very strange bug/error. 1. The error occurs only for a specific input dataset that has the same properties as hundreds of other input datasets that run...

Hi, Are there recommended scripts / process for calculating TPM or FPKM from the zUMIs counts data? Thanks

Workflow question

1

Hi, What is the recommended workflow for generating the required BAM files? Also, what is the recommended tools for clustering wgbs samples? ie, samples from different tissues and then unbiased...

CRAM input

1

Hi, Does DeepMosaic work with CRAM format input?

subtract documentation

6

Hi, subtract says that metadata columns of x are propagated, but that doesn't seem to be happening: "The names and metadata columns on x are propagated to the result." ```...