Release: BAM to plink

[teepean]

MT23 right here... .bam and .bai

https://www.ebi.ac.uk/ena/browser/view/PRJEB54894

Did you choose this one? The other bams for MT23 are unaligned.

MT23.fastq.combined.fq.prefixed.mapped.mappedonly.sorted.qF.sorted.cleaned.merged_rmdup.clean.RG_sort.rescaled.bam

Yeah this one exactly...

So what is the exact problem?

[teepean]

Yeah this one exactly...

So what is the exact problem?

.bim file less than 50 megabytes, unable to merge in 1240K dataset

That's the 1240K dataset bim so I am not sure what kind of problems that might have.

[teepean]

Can anyone help me with this problem?
https://files.catbox.moe/y4yd4d.jpg

You need to download pileupCaller

https://github.com/stschiff/sequenceTools

And extract the executable to the same directory where adna_to_dataset is and make it executable.

[teepean]

Can anyone help me with this problem?
https://files.catbox.moe/y4yd4d.jpg

You need to download pileupCaller

https://github.com/stschiff/sequenceTools

And extract the executable to the same directory where adna_to_dataset is and make it executable.

still doesn't work

Do you get the same error message? Could you list the directory of the program with ls -la and provide a screenshot, please.

[teepean]

First download this and extract it to your home directory. Make sure it creates a folder called adna_to_dataset-v.0.7

https://github.com/teepean/adna_to_datas.../v.0.7.zip

Then download this:

https://github.com/stschiff/sequenceTool...ller-Linux

Extract it to adna_to_dataset-v.0.7 folder, rename it to pileupCaller and then make it executable (chmod +x pileupCaller )

[Anglesqueville]

I stuck with version 0.5, which works great (well done!). What do the latest updates bring (version 0.7 if I'm not mistaken)?

[teepean]

I stuck with version 0.5, which works great (well done!). What do the latest updates bring (version 0.7 if I'm not mistaken)?

Just small updates bugfixes. I should update samtools to the latest version as mpileup is about 20% faster. Maybe next week.

[Light]

Colab Notebook:- https://colab.research.google.com/drive/...sp=sharing

[Light]

@teepean

The package and .sh file from GitHub seems to run into errors on Colab, could you see what might be causing the error?
PileupCaller not built in Colab? Something like that I'm finding

[teepean]

@teepean

The package and .sh file from GitHub seems to run into errors on Colab, could you see what might be causing the error?
PileupCaller not built in Colab? Something like that I'm finding

BAMs should go to this folder:

/content/adna_to_dataset/adna_to_dataset-v.0.7/source

It is missing samtools and pileupCaller.

This:

!chmod +x /content/adna_to_dataset/adna_to_dataset-v.0.7/bam_to_plink.sh
!bash /content/adna_to_dataset/adna_to_dataset-v.0.7/bam_to_plink.sh

Should be changed to:

!chmod +x /content/adna_to_dataset/adna_to_dataset-v.0.7/bam_to_plink.sh
!cd /content/adna_to_dataset/adna_to_dataset-v.0.7
!bash ./bam_to_plink.sh

I have never used colab so I am not sure why it is not detecting the references.

[Light]

It detects reference after changing the directory of references in .sh file, but my main error is it not finding PileupCaller and manual installation is also running into issues

[Light]

Do you know the general Linux commands to convert BAM to BED using Samtools/Bedtools? I haven't found a working tutorial, but in that case I could create direct code from Samtools

[teepean]

It detects reference after changing the directory of references in .sh file, but my main error is it not finding PileupCaller and manual installation is also running into issues

You have to download pileupCaller from here:

https://github.com/stschiff/sequenceTools

I don't know how to install samtools when using colab.

[Light]

Colab works the same way but kind of on cloud system runtime than local, so commands should be the same. If you have something for Linux/Python environment then I could create a code in Colab directly

[teepean]

Colab works the same way but kind of on cloud system runtime than local, so commands should be the same. If you have something for Linux/Python environment then I could create a code in Colab directly

Both samtools and pileupCaller are required. PileupCaller binary can be just downloaded and made executable but I am not sure how to install samtools unless there is apt or something similar available. If conda can be used then it it's just:

conda install bioconda::samtools
conda install bioconda::sequencetools