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Old 04-08-2019, 04:53 PM   #1
seek_help_or_be_help
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Thumbs up Gave the Wrong Indexes for WGS... but I know them!

I recently sent off 100+ genomes to be whole genome sequenced and I sent the incorrect ones for a couple... but I have the correct ones! Is there a method which I can use them to determine my sequences

Currently, I have three lane files with sequences but how can I determine which sequences belong to what sample. I tried using process_rad tags with my barcodes but cant retrieve my sequences... I see the tags when I use grep but is there a more efficient way of doing this???

Thanks...
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Old 04-08-2019, 06:39 PM   #2
luc
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Sorry, I do not fully understand what type of information you have and what you are looking to retrieve.
Do you see the index read sequences in the read headers?
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Old 04-08-2019, 08:03 PM   #3
seek_help_or_be_help
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Sorry. Yes I see some but they contain Ns.

I believe that the sequencing company didnt cleaned up the incorrect indexes for since they contain Ns in the index headers.


I have sequence data for the lanes I ran. I am looking to retrieve the sequences that match my unique indexes as they pertain to specific individuals. They each have unique IDs. So I am trying to identify which sequences in each lane pertain to each sample.

@G98558:222:XXXXXXX:6:1101:6258:1397 1:N:0:NCCCCTCG+NGATCTCG


Sample I TATAGCAT GTAGTAT
Sample II XXXXXXX XXXXXXX
Sample III XXXXXXX XXXXXXX
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Old 04-08-2019, 09:50 PM   #4
SNPsaurus
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It sounds to me like the reads were demultiplexed, but you had given incorrect index sequences for a few samples, so those reads are still in the Undetermined file and you want to extract them? Is that right?

I'd say if you can see them with grep you should just let that run and it would be faster than figuring out the optimal way to extract them. But it is curious that process_rad_tags doesn't see them. Have you configured it for dual indexes rather than inline RAD barcodes?
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Old 04-08-2019, 10:39 PM   #5
seek_help_or_be_help
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Yes. Sorry my wording is awful.

I can see them in the sequences, not the header... but I'm taking that with a grain of salt which is why I'm wondering if there is a way to do it differently.

I'm not sure how to configure it for dual indexes, unless if you mean providing a file with index 1 and then index 2 which I have.
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Old 04-09-2019, 09:07 AM   #6
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It would be helpful to say exactly what libraries you made and then paste some example sequences of what you got back. Were most samples successfully demultiplexed? What do those reads look like?
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