Comments (5)
mizraelson
commented on August 18, 2024
1
Hi,
You can use an arbitrary header, but keep in mind that it will be used as a gene name in the output tables. If you choose to use '|' as a separator, only the first element will be assigned as a name. For example: '> TRBV14-3|homosapiens|SRR0309337'.
Sincerely,
Mark
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mizraelson
commented on August 18, 2024
Hi,
MiXCR should work with any species but requires the correct reference. This article will guide you through the process of creating a reference for non-model organisms, provided you have FASTA files with all gene segments.
Sincerely,
Mark
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silvia1234567890
commented on August 18, 2024
Great, thank you so much.
Just one question, the headers of the gene segments need to be in a specific format?
I checked that link and in the example they are:
>IGHV12-348
GATGCTGGAGTTATCCAGTCA...
>IGHJJ1-528
TAACAACCAGGCCCAG...
And I have fasta files like this:
>aOncmyk_Chr8_CM023226.2_TRAV4-6_F_61345213_61345541
GTGACAGTCTTCAGAC...
>aOncmyk_Chr8_NC_048572_RS_TRAJ1_F_61944197_61944292
AGTGACTGGAACAGGA...
Thank you
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silvia1234567890
commented on August 18, 2024
Please, I need a confirmation if "yes" or "no" and I will close this issue, thank you!
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silvia1234567890
commented on August 18, 2024
Oh ok, thank you so much for your help!!
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