Demultiplexing bam file
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14 months ago
hasani.iut6 ▴ 60

Hi to everyone,

I have NIPT data from multiple samples which are sequenced by Iontorrent. All of them are aligned together using bowtie. I want to separate every sample from the aligned bam file which consists of all samples together. Part of the header of the bam file is:

@HD VN:1.4  GO:none SO:coordinate
@RG ID:QDQDB    PL:IONTORRENT   PU:s5/540/Q35S04/08/DAIL00351   FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTG DT:2023-05-04T05:36:13-0300 SM:13.02.1402_POOL2 KS:TCAG CN:ParsGene/S5XL-GALAXY
@RG ID:QDQDB.1  PL:IONTORRENT   PU:s5/540/Q35S04/08/DAIL00351   FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTG DT:2023-05-04T05:50:01-0300 SM:13.02.1402_POOL2 KS:TCAG CN:ParsGene/S5XL-GALAXY

how can I do that?

demultiplexing bam_file Iontorrent • 901 views
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I want to separate every sample

I don't understand. In your header there is only one sample : "13.02.1402_POOL2"

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so why the size of bam file is 40 gig?

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you don't talk about the size in your question

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Yes, you're right, I know the bam file consists of multiple samples (It should be between 30 to 40 samples) and the size of the bam file is about 45GIG.

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Part of the header of the bam file

So perhaps there are more samples.

hasani.iut6: grep "SM*" header_of_bam. Is there more than one unique ID there?

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No. All of the Ids are "13.02.1402_POOL2". Do you think my bam file is not correct?

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