User: segrossk

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segrossk20
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Posts by segrossk

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Comment: C: bcl2fastq with xGen Dual Index UMI Adapters to produce 3 read and 2 index fastqs
... genomax, adding the --mask-short-adapter-reads 0 option to the bcl2fastq commands in the original post worked perfectly. I would not have thought of using that option. Thank you so much! ...
written 12 months ago by segrossk20
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Comment: C: bcl2fastq with xGen Dual Index UMI Adapters to produce 3 read and 2 index fastqs
... genomax: Thank you for pointing out your post, which I came across and it did not resolve my issue of bcl2fastq placing 9bp N's instead of the sequence in the UMI files. The options that I use for bcl2fastq does everything correct except for the R2 fastq containing the UMI read. The R1 and R4 76bp r ...
written 12 months ago by segrossk20
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bcl2fastq with xGen Dual Index UMI Adapters to produce 3 read and 2 index fastqs
... I have RNA-Seq from Illumina HiSeq using IDT xGen Dual Index UMI Adapters, where the UMI are added on the i7 index. Typically, I would use a pipeline using Picard which is recommended by IDT. However, I was hoping to use bcl2fastq (v2.17.1.14) to immediately produce fastqs. Below is the molecular b ...
rna-seq written 12 months ago by segrossk20 • updated 9 months ago by gloria.lam0

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