Ian Hoskins

Upon further investigation, insert size=0 is output when including the --no-discordant flag. Is this set when the mate information is not available? With the exception of the few reads with...

Given https://github.com/BenLangmead/bowtie2/issues/344 I suspect there is some interaction between the --no-discordant option and insert size calculation.

@BenLangmead thanks for taking a look. If I run without the --no-discordant option I get normal TLEN fields. It is only with this option when I get pairs that have...

I think this is related to my understanding of --rf. Does this flag mean: 1) first segment maps to reverse strand and second segment maps to forward strand, or 2)...

I note that I ran Bayeshammer on FASTQs where I had edited the quals at the termini of reads to be the same. It is possible the issue arises with...

For completeness, here are the FASTQ records before input to Bayeshammer: ``` @COOPER:281:H2HJ3BBXY:6:1101:1184:44377 RG:Z:CBS1_31_S10_L006_R GCTTCAGTGGGCACGGGCGGCACCATCACNGGCATTGCCAGGAAGCTGAAGGAGAAGTGTCCTGGATGCACGATCATTNGGGTGNNTCCNGNAGGGTCCATCCTCGCAGAGCCCGAAGAGCTGANCCAGACGCAGCAGACAACCTAC + SSSSSSSSSSSSSSSSSSJFJJJFJ-FFJ#AFJJJ7-FJJF

@andrewprzh this seems like a fatal error for users running Bayeshammer only. Can you reproduce? Let me know if I can provide any files.

A little late on this discussion, but I too use the MD tag despite its shortcomings. I believe the pysam.AlignedSegment.get_aligned_pairs() function relies on this tag as well, which is a...

@MiguelCos @incle440 I too experienced inconsistent results between the cluster profiles shown in the output PDF and the profiles I viewed manually for entities in an assigned cluster. My normalization...

@ethan-redmond I was able to install clust through Conda using a very simple configuration: ``` name: clust channels: - conda-forge - bioconda - defaults dependencies: - python>=3 - clust ```