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indexcov: usage with long reads ?

1

Hi, would you expect this to work for long reads ? The scaling looks great in your png example, with most values around 1. I see most values are low...

colindaven

covstats supporting cram

10

Any chance of covstats supporting cram format? Unsurprisingly, when I tried I got an error: `$ goleft covstats input.cram` ```coverage insert_mean insert_sd insert_5th insert_95th template_mean template_sd pct_unmapped pct_bad_reads pct_duplicate pct_proper_pair...

hdashnow

Indexcov errors

2

Hi @brentp I have been trying to run Indexcov on a directory of bams using this command goleft indexcov --directory /spaces/emma/goleft/Results /dataJ/build38/datasets/baylor/combined_bams/*.bam and I am getting the following errors..this is...

emmakwiener

goleft_linux64 depth --maxmeandepth 100 --mincov 0 --q 20 --stats --reference $reference --processes 20 --bed Agrotis_ipsilon.GCA_004193855.1_ASM419385v1_genomic.CDS.bed --prefix $prefix $bam 2020/09/30 19:03:32 open P14913_125_S47_L003.q20.CDS.PNFC01000001.1-121292-121422.tmp.callable.bed: no such file or directory make these before...

bioinfowheat

Please correct the typo in README (gitub without 'h' in https://gitub.com/golang/go).

przemekl

coverage of the customized genome

2

Dear Brent; I build a customized genome sequence by adding a new sequence "VectorA" (~ 10kb) to hg19, and I would like to have coverage of the VectorA via your...

weizhu365

Feature request: New option --exclude for indexsplit

1

Hi Brent, I would like to propose a new option for `goleft indexsplit` (and would have implemented it myself if my Go was any good): `--exclude` to be able to...

andreas-wilm

indexcov support for csi indexes

2

Hi @brentp. Any chance to add support for CSI indexes for indexcov? Generating lots of assemblies, and many have larger scaffolds, which require the CSI rather than BAI...

mcshane

Differential header stringency depending on file format

4

I noticed this in I'm observing differential error checking depending on whether or not the input file is a CRAM or a BAM. The files in question have multiple sample...

ernfrid

Suggestions : paths ; case/control

3

Hi Brent , here are two suggestions for indexcov - using a file containing the path to the bams (to avoid something like `xargs` ) - if we could include...

lindenb