SAMtoBAM

Overlapping deletions/insertions

8

Hi there, I have noticed several times that there will be a cluster of small-ish deletions or insertions that appear to frequently overlap one another. What I can say with...

raw fraction commonly show many positions with 0.5

3

Hi there, I am currently running tombo on a couple of species and what I find is that many of the positions have 0.5 as the raw fraction of reads...

output conversion to SAM/BAM file

4

Hi there, I have a polyploid genome that I want to map to a haploid reference and want to calculate the depth/number of contigs aligning at each region. Is there...

searching database for any duplicates genomes

3

Hi there I have received genomes from numerous sources, some previously public, some not but I don't know which So I have a set of genomes and want to see...

taxonomy/prelim_map.txt: No such file or directory

3

scripts/kraken-build --build --db custom_db/ Kraken build set to minimize disk writes. Creating k-mer set (step 1 of 6)... Found jellyfish v1.1.11 Hash size not specified, using '46074880' K-mer set created....

Hi there Would it possible to allow multiple target and/or queries in the same synteny plot? It would be really handy for me at least Thanks

HISAT alignment, sam, bam, sorted.bam steps

1

Hi there I am trying braker3 at the moment and see that the RNAseq alignment step appears to perform the alignment to sam, compression to bam and sorting in 3...

best_by_compleasm.py unable to find compleasm.py

1

Hi there I am trying to add the busco/compleasm step to my pipeline as adding rnaseq data appears to be making my output too conservative I am using a conda...

Hi Emile Been running `starfish coverage` on some elements but it isn't working on elements with a header such as that contains a space Looks like the discrepancy is between...

Hi there In the [step-by-step pipeline](https://github.com/egluckthaler/starfish/wiki/Step-by-step-tutorial) there are several lines that use ```grep -v '#'``` to get rid of some headers/notes in certain files I think this can be changed...