1. Homo Sapiens:
2. Mus Musculus:
3. Custom genome model (.BrowGenModel format):
4. Custom genome model (.gb genebank format):
Generate new custom genome model:
1. Enter the species name:
2. Choose chomosomes to be included (?):
3. Load genome sequence file (.2bit format) (?):
4. Import only KNOWN genes/transcripts?
5. Import readthrough transcripts?
6. Import confidence level 3 transcripts?
7. Import ENSEMBL gene id instead of gene symbols?
8. Load gene model (GENCODE .gtf format, takes several minutes) (?):
9. Save the genome model in .BrowGenModel format (?):
2. Download genome sequence hg38.2bit, then upload: (?):
3. FASTQ files (Read 1, Read 2 alternating):
4. Optional: Position and sequence of read filter: (?) bp,
5. Forward mapping start position in reads: (?) bp
6. Forward mapping length: bp
7. Reverse mapping length: bp
8. Max forward/reverse span: bp
9. How to register ambiguous hits?
10. How much memory can BrowserGenome use? (?)
11. Keep index in memory for next alignment:
12.
?
+
-
Process mapped data:
bp
Filter all tracks based on first track:
Design deep sequencing primers for specific target regions (Use with OutKnocker.org):
1. Download genome (e.g. hg38.2bit), then upload:
2. Enter target sequences of interest (e.g. CRISPR target sites, 23-mers or longer):
3.
Quantify counts of annotated genes:
1. Count hits on
2. Normalize hit numbers to total hit numbers
3. Normalize hit numbers to cumulative exon length
4. Export the data (?):
Visualize logarithmic mapping depth
Save selected track:
(5 bytes per mapped read)
(ca. 40 bytes per mapped read, may take a few minutes)
BrowserGenome 1.1 For non-commercial, non-diagnostics use only.
