Spliiting the bam files into separate samples ,tophat2
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9 weeks ago
Dixi • 0

Hi everyone,

I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files for all the samples. Can I spilt them from the one I have or I have to do tophat2 for all the samples separately? If yes, how to do it.

I need them for FRASER (spilicing detction) I would also appreciate if anyone used FRASER before could help me a bit to get started. I am working with plant data for the first time.

Thanks.

plant_sequence fraser rna splicing tophat2 data sequencing • 240 views
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Is this 12 independent samples? If so then just repeat the alignment for each separately. This will probably be finished before you have put code together to properly and reliable split the samples from one bam file. It is anyway not very meaningful to combine samples into a single file.

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Thank you for your reply. I have 3 replicates of each treatment. so 4 treatments x 3 replicates =12 files.

Should I merge the replicates or just go for separate alignment for each sample?

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