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Hello,
Can the same pipeline be used for cDNA sequencing as well?
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Hi, we have sequenced 5 samples' scRNA-seq in your company and when I got the data, I found that there are multiple directories under each sample and for each sub-directory, there are also two pairs o…
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Is pychopper compatible with with the new SQK-PCB114.24 kit. Will the '-k PCS111' work ?
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Hi there,
On the [ONT community website](https://community.nanoporetech.com/docs/prepare/library_prep_protocols/ligation-sequencing-v14-direct-cdna-sequencing/v/dcs_9187_v114_revh_19apr2023/downstr…
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Two attributes (cDNA Length and cDNA Offset) that were accidentally included in this initial version of the template. These are optional attributes and can be ignored by users currently, but we should…
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N.B. These plates will enter the existing 10X pipeline(s). There is an existing way to get these samples into the LIMS - but, I think we need this new manifest because we need the individual donor inf…
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Hi Zhenyu,
I noticed in the script S02.umi.process.one.sh, you used minimap2 for mapping to the reference genome and then used salmon for quantification. Additionally, it seems that for the referen…
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Thank you for sharing your code and data :)
However, I encountered an issue while examining the cDNA data. I noticed that several PDB entries, which provide corresponding MSAs and FASTA files, are n…
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Hi,
In both single-cell and bulk RNA sequencing, we use UMIs (Unique Molecular Identifiers). Two reads with the same UMI correspond to the same cDNA molecule. It would be great if we could feed inf…
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Hello,
Can the same pipeline be used for cDNA sequencing as well? I have the fastq reads and the reference genome and transcriptome fasta sequences.
Thank you.