How to generate the i5 of fastq file?

[Joyjoyjoyc]

Hi there,
I'm new here, and thanks for developing such a useful tool, I wonder how to generate the i5 of fastq file?

[chenweng1991]

Hi, i5 can be generated by letting the demultiplexing software be aware of generating index reads For example, using bcl2fastq --create-fastq-for-index-reads or setting sample sheet using bcl-convert Alternatively, Cellranger mkfastq can help generate index fastq as well https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/inputs/generating-fastqs-mkfastq Hope that helps Chen

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On Wed, Dec 25, 2024 at 5:58 AM Joyjoyjoyc ***@***.***> wrote: Hi there, I'm new here, and thanks for developing such a useful tool, I wonder how to generate the i5 of fastq file? — Reply to this email directly, view it on GitHub <#8>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKKAEACA5ZW6PU3YZDM4JJ32HKFVRAVCNFSM6AAAAABUF3PR62VHI2DSMVQWIX3LMV43ASLTON2WKOZSG42TQNZSHE4DCNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Joyjoyjoyc]

Got it. Thanks for your quick reply.

---- Replied Message ---- | From | Chen ***@***.***> | | Date | 12/25/2024 19:20 | | To | chenweng1991/redeemV ***@***.***> | | Cc | Joyjoyjoyc ***@***.***>, Author ***@***.***> | | Subject | Re: [chenweng1991/redeemV] How to generate the i5 of fastq file? (Issue #8) | Hi, i5 can be generated by letting the demultiplexing software be aware of generating index reads For example, using bcl2fastq --create-fastq-for-index-reads or setting sample sheet using bcl-convert Alternatively, Cellranger mkfastq can help generate index fastq as well https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/inputs/generating-fastqs-mkfastq Hope that helps Chen

On Wed, Dec 25, 2024 at 5:58 AM Joyjoyjoyc ***@***.***> wrote: Hi there, I'm new here, and thanks for developing such a useful tool, I wonder how to generate the i5 of fastq file? — Reply to this email directly, view it on GitHub <#8>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKKAEACA5ZW6PU3YZDM4JJ32HKFVRAVCNFSM6AAAAABUF3PR62VHI2DSMVQWIX3LMV43ASLTON2WKOZSG42TQNZSHE4DCNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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