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ulelab / ultraplex

Ultra-fast 5' and 3' demultiplexer
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Test Ultraplex on PacBio sequencing data #43

Open gooodle opened 1 year ago

gooodle commented 1 year ago

I tried the program on PacBio hifi reads, which were for amplicon sequencing of some plant DNA samples, barcoded on both ends. The reason is that LIMA generated very simple report missing a lot of information of my interest, such as how many reads only have one barcode, and how many reads are without any barcodes.

I followed the instruction, gzipped the fastq file, and prepared barcode .csv file (first column 5' barcode, second column 3' barcode, both 16base long). It ran quite fast, but somehow the .log file stated that there was only 1 read successfully assigned to a sample file.

I understand the 2 default illumina adaptors are not present in the reads, I am guessing that might be part of the reason leading to the failure? or Ultraplex can't be used on PacBio reads at all?

Thanks.

Delayed-Gitification commented 1 year ago

I'm afraid I have no experience with pacbio data so I cannot provide any detailed instructions on this. Apologies!

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From: gooodle @.> Sent: Monday, May 29, 2023 11:00:00 PM To: ulelab/ultraplex @.> Cc: Subscribed @.***> Subject: [ulelab/ultraplex] Test Ultraplex on PacBio sequencing data (Issue #43)

I tried the program on PacBio hifi reads, which were for amplicon sequencing of some plant DNA samples, barcoded on both ends. The reason is that LIMA generated very simple report missing a lot of information of my interest, such as how many reads only have one barcode, and how many reads are without any barcodes.

I followed the instruction, gzipped the fastq file, and prepared barcode .csv file (first column 5' barcode, second column 3' barcode, both 16base long). It ran quite fast, but somehow the .log file stated that there was only 1 read successfully assigned to a sample file.

I understand the 2 default illumina adaptors are not present in the reads, I am guessing that might be part of the reason leading to the failure? or Ultraplex can't be used on PacBio reads at all?

Thanks.

— Reply to this email directly, view it on GitHubhttps://github.com/ulelab/ultraplex/issues/43, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APJN63R3HBM2GMZPSU2SWZTXIUL6BANCNFSM6AAAAAAYTGKM2Q. You are receiving this because you are subscribed to this thread.Message ID: @.***>