Raw data for chromosome 21
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2.6 years ago
tamara912 • 0

Hi!

I downloaded from the European Nucleotide Archive raw data (fastq) for human chromosome 21. It was indicated that the library is WCS and that the data is only for chr21. I mapped the data with Bowtie2 in Galaxy and I got the bam file containing all chromosomes, instead only chr 21.

So, my question is why I have all the chromosomes in my bam file?

I tried to filter that bam for only chr21, but the alignment is very bad so I suppose that this approach is not very good.

Thank you in advance.

bam file chromosomes sequencing raw data WCS • 780 views
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Please give some details. Which dataset is this? What is WCS, do you mean WGS like whole genome sequencing? Please provide the link to the dataset.

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The link to the dataset: https://www.ebi.ac.uk/ena/data/view/DRR000546

No, I mean like WCS: Random sequencing of a whole chromosome or other replicon isolated from a genome. (This is from ENA training modules website)

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Can you post a link for tutorial page?

If the data is only for chr 21 then perhaps you should only be aligning against that in first place.

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Thank you very much! I didn't consider that using a whole reference genome is a problem...

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Have you checked percent aligned reads per chromosome?

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Hm, not yet. I will try it if it can be done in Galaxy

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