Online service for fastq and BAM conversion

[vbnetkhio]

https://usegalaxy.org/

free online service for fastq and BAM conversion, and some other tools too

[Lucas]

https://usegalaxy.org/

free online service for fastq and BAM conversion, and some other tools too

Shitload of various tools but where is Fastq to BAM converter which is the most important?

[vbnetkhio]

Shitload of various tools but where is Fastq to BAM converter which is the most important?

BWA MEM is there. some others too (regular bwa etc.), but I think there's no need to look further:

https://www.biostars.org/p/117225/

The mapping rates were:
bowtie2: 30%
bwa aln: 25%
bwa mem: 85%

Of course each of these mapping rates are for default settings that can be changed (see comments down) - but that's where we always start. From those it looks like bwa mem goes a step further and will find alignments where other methods have already given up.

btw: Arza used aln for those Goth samples, and they turned out fine in G25. so mem can only be better,

[vbnetkhio]

Shitload of various tools but where is Fastq to BAM converter which is the most important?

there are multiple BAM to vcf tools too.

I think "bcftools mpileup" and then "bcftools call" is the best.

[Peterski]

Nice website, thanks for the link!

[Lucas]

there are multiple BAM to vcf tools too.

I think "bcftools mpileup" and then "bcftools call" is the best.

Did you check at least some fastq in it? How long it takes?

[vbnetkhio]

Did you check at least some fastq in it? How long it takes?

Yes, that's how i converted the Maslomecz file. It was very fast, maybe half an hour.

[Lucas]

Yes, that's how i converted the Maslomecz file. It was very fast, maybe half an hour.

Can you post pipeline steps?

[vbnetkhio]

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

[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
-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

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