Data · dataset · 2025
Mouse cerebellum .bam files
Listed in ScienceDB
The original .fast5 file comes from the article “Double and single stranded detection of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore sequencing”.
Description
Raw .fast5 files were converted to .pod5 using pod5-file-format with command "pod5 convert fast5 -t $(nproc) $indir/*.fast5 -o $outdir". .Pod5 files were modification called using Dorado v0.8.1 and v0.5.1 with command "dorado basecaller $BASECALLING_MODEL $indir --modified-bases-mode $MODCALLING_MODEL --reference $reffile --device cuda:all --verbose --batchsize 0 --recursive > $outdir", where model file is "dna_r10.4.1_e8.2_400bps_sup@v4.3.0" or "dna_r10.4.1_e8.2_400bps_hac@v4.3.0", followed by sorting ,viewing (samtools view -h -F 4079), and indexing with Samtools.
The reference genome used for alignment is the GRCh38 reference genome (GenBank assembly ID GCA_000001405.15).
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.30576 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Sequencing 75%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.30576 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license_text | source · scidb cn | connector:scidb_cn@1.0.0 | |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |