Interpreting bam-files from Prokka annotation

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5.1 years ago

Hansen_869 ▴ 80

Hi!

I have used Prokka on some bins, which I found with Maxbin2. On the annotated genes, I then used BWA together with the raw FASTQ files, to obtain a BAM file. Now, how do I interpret the bam file? The main goal is to find the depth for each of the genes that were annotated with Prokka.

Thanks!

bam samtools prokka bwa • 1.2k views

ADD COMMENT • link 5.1 years ago by Hansen_869 ▴ 80

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Instead of posting basically the same question twice you might consider investing more effort into one of them, adding details and context. People seem to lack the necessary information to help you. Finding depth of genes

ADD REPLY • link 5.1 years ago by ATpoint 85k

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Thanks for your response. In the first post I was asking for the approach of finding the depth, which I have now decided. Now I just need help interpreting the BAM-file. So i find the two posts quite different. But people are free to ask for further information if in doubt.

ADD REPLY • link 5.1 years ago by Hansen_869 ▴ 80

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It's basically the same question. I started to reply to the other one but wasn't sure if my advice was the best. There are several tools to count how many reads span each gene, from the simple htseq-count to RSEM and stringTie.

ADD REPLY • link 5.1 years ago by Asaf 10k

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Thanks for your reply. I will take down the other post then, to avoid confusion. Do these tools just require a BAM-file as input?

ADD REPLY • link 5.1 years ago by Hansen_869 ▴ 80

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