Online service for fastq and BAM conversion

[vbnetkhio]

Thanks. If selection as ref hg38 would be better or not?

I think not, all software, gedmatch, g25, still uses hg19, also if you use that list of 23andme/ftdna positions i mentioned, it's also in hg19

[Lucas]

Ok started conversion of some Chad sample which I hesitated before because of enormous size

[Lucas]

1)upload the fastq file, it will be added to your "history"

2) search for the "Map with BWA-MEM" tool
-select "Human (Homo Sapiens) (b37): hg19" as the reference genome
-select single end reads

What about paired fastq, this time paired end reads? Or you convert them separately?

[vbnetkhio]

What about paired fastq, this time paired end reads? Or you convert them separately?

Idk, i didn't encounter them yet. If there are 2 fastq files of the same sample is that paired? or could it just be a sample split into 2 files?

I just converted those separately and then merged them in the end.

[Lucas]

Idk, i didn't encounter them yet. If there are 2 fastq files of the same sample is that paired? or could it just be a sample split into 2 files?

I just converted those separately and then merged them in the end.

Ok I tried paired and has error that no index... Now I convert one from the pair and it seems is processed. What you use here for merging bams?

[vbnetkhio]

Ok I tried paired and has error that no index... Now I convert one from the pair and it seems is processed. What you use here for merging bams?

I just convert them separately and merge them in the end with dnakitstudio

[Lucas]

I just convert them separately and merge them in the end with dnakitstudio

Last question if I can close browser and it still will be processed on my galaxy account?

[vbnetkhio]

Last question if I can close browser and it still will be processed on my galaxy account?

Yes, only uploading in proccess gets cancelled if you close the browser

[Peterski]

1)upload the fastq file, it will be added to your "history"

2) search for the "Map with BWA-MEM" tool
-select "Human (Homo Sapiens) (b37): hg19" as the reference genome
-select single end reads
-select your fastq from the history
-execute

3) search for "bcftools mpileup"
-select your bam output from the first step
-select "Human (Homo Sapiens): hg19" as the ref genome
-for faster conversion and a smaller vcf output, i also upload a text file with ftdna and 23andme positions only.
The format is "chromosome position" tab separated, one per line.
E.g.
1 84582272
1 25797421
I think i had some problems with 0 and MT chromosomes so just remove those if you get errors.
-then go Restrict to - regions - operate on regions specified in a history dataset and select that text file you uploaded
-execute

4)go to "bcftools call"
-select your bcf file from the previous step
-select uncompressed vcf output
-execute

Are there, currently, any interesting samples in FASTQ worth converting ???

[vbnetkhio]

Are there, currently, any interesting samples in FASTQ worth converting ???

The Polish Gothic/Medieval samples, and 2 or 3 Hungarian conqueror studies. (They are all low quality, but there's a lot of them, so they can be merged by period/arch. site)

I tried the Arpad dinasty fastqs, but they seem to include only y and mtdna. And those 200 Macedonians have very few snps.