gevro
gevro
Hi, Is there any way to do this? This would be simpler than converting PacBio BAM files to fastq, and then somehow integrating the info from the original PacBio BAM...
Hi, I'm getting this error. What is the cause of this? Thanks. singularity run -W /data -B /scratch/projects/bin/deepconsensus/model:/model -B `pwd` /scratch/projects/bin/deepconsensus/deepconsensus_0.3.1.sif deepconsensus run --batch_size=1024 --batch_zmws=100 --cpus 1 --max_passes 20 --subreads_to_ccs=blah.subreads_to_ccs.0018.bam...
Hi, I'm getting the below error: ``` Total params: 9,525,067 Trainable params: 9,525,067 Non-trainable params: 0 _________________________________________________________________ Traceback (most recent call last): File "/home/user01/.local/lib/python3.8/site-packages/tensorflow/python/training/saving/saveable_object_util.py", line 130, in restore assigned_variable =...
Hi, It seems that CallMolecularConsensusReads collapses the UMI sequence and assigns 'N' to UMI bases that are ambiguous based on the constituent reads. I couldn't find where this was documented,...
Hi, Does GroupReadsByUmi require all sequences to be aligned to the same strand? I assume yes, but the documentation doesn't state this explicitly. Thanks.
Hi, I read the documentation of this in FilterConsensusReads and issue #596, but I'm still a bit unclear about this. My pipeline is: align to BAM file -> AnnotateBamWithUmis ->...
Hi, There is no default value for min-base-quality in FilterConsensusReads, and I'm a bit unclear on the exact format of setting this, and also how consensus base qualities are encoded...
minimap2 calculates a new tag 'cs' that encodes SNPs/Indels more easy to interpret than MD tag +CIGAR. Is there any plan to create a samtools command to generate a cs...
Hi, Are you aware of any CHM13 based imputation panels?
Hi, It would be super useful to activate both the View->In other genome, and the Liftover tools in the v1.0 and v1.1 UCSC browsers, both between them and to hg19/h38....