-
Hi hisat-3n developers,
Thank you for building this wonderful aligner!
I am working on using hisat-3n to align all the single-cell DNA methylome and multiome data generated by the [snmC-seq2 (D…
-
# Design
## Additions
For Assay
MUST Use
mCT-seq [EFO:0030060]
"cell" or "nucleus"
MERFISH [EFO:0008992]
"na"
…
-
## Describe the bug
When attempting to download a dataset using the `cellxgene_census` Python library, the function `download_source_h5ad` fails with a `KeyError` indicating an 'Unknown dataset_id'…
-
The 2 methylation (snmC-seq) datasets here: ae1420fe-6630-46ed-8b3d-cc6056a66467
update to: EFO:0030027 (snmC-Seq2)
The 3 datasets here: 00109df5-7810-4542-8db5-2288c46e0424
update to: EFO:003002…
-
See [schema reference](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/schema.md#suspension_type).
1. `cellxgene-schema `MUST warn and fail if the corresponding assa…
-
Researchers need to be aware of which data are single-cell vs single-nucleus so that they can take special care to ensure proper integration.
Most contributors don't provide it automatically because …
-
For new term requests, please provide the following information:
## Preferred term label
snmC-Seq2
## Synonyms
single nucleus methylcytosine sequencing v2
## Textual definition
A pro…
-
The assay type for the methylation datasets (see below) was set as "methylation profiling (EFO:0000751)". However, according to the paper the specific assay is snmC-seq for which there is an appropria…
-
Hello,
I am running yap demultiplex with YAP with the following command:
yap demultiplex --fastq_pattern "/path/to/fastq_files/snmC-seq2/*/*fastq.gz" --output_dir /outdir/demux_output --config_p…
-
## Preferred term label
methyl-c sequencing assay
## Synonyms
mC-seq2
## Textual definition
A sequencing assay (library preparation method) that involves fragmentation of genomic DNA fo…