paleomix

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biobambam2 instead of picard-tools?

10

Is it feasible to switch to biobambam2 for the duplicate marking and BAM validation steps? One of the main problems we have with large paleomix runs (e.g. 100 samples) is...

sameoldmike

Should the .rmdup.collapsed.bam and .rmdup.normal.bam be merged?

1

Hi Mikkel, I have used your pipeline in my Master's thesis to trim and map my target capture reads. The pipeline has run without errors, and as a result I...

vitalirazumov

About the MinQuality setting

6

Hi Mikkel, I am doing a set of stringency trails, to calculate the number of hits under different "MinQuality" settings using paleomix pipeline. The makefile document and paleomix scripts were...

ztang040

Please switch to Python3

22

Hi, Debian is currently debating the support of Python2 which is marked end of life in 2020 (which is only one release cycle away. I'd recommend to switch to Python3...

tillea

documentation for paloemix phylo pipeline

1

Dear Mikkel, After successfully using your fantastic paloemix bam_pipeline to generate bam files of my genomes, I am trying to used the phylo pipeline. However, I am struggling to make...

siriusb-nox

Alignment to sequence variation graph?

1

[Rui Martiniano and others](https://www.biorxiv.org/content/10.1101/782755v1) have shown that mapping aDNA reads to a variation graph can substantially reduce reference bias. It would be great if vg could be included as a...

nwales

Trimming first 6-8 bp of read 1

2

Hi Mikkel, I hope you are doing well! I'm processing some new data and I wondered if there a way to remove the first N bp of read 1. In...

nwales

Receieved a NodeError while running the pipeline

1

Hello! I ran into an error as following while trying to running my sample. 38 INFO Validating FASTA files 16:44:38 INFO Building BAM pipeline for 'N_chinensis-novo.yaml' 16:44:38 INFO Running BAM...

farahwar

Paleomix output reads folder no fastq reads

2

Hi Thanks for your useful tool. It is much more convenience for mapping. In my side, I use AdapterRemoval2 to trim the ancient PE reads, and have truncated reads. Then...

xuefenfei712

Can BWA use aln to shorter than 70bp and mem to longer using bam_pipline

3

Hi, I am running paleomix bam_pipeline, I want to use bwa aln when the reads shorter than 70bp, and when read longer than 70bp, using bwa mem algorithm, I want...

jiangzy26