Plot read coverage for a GRanges objectYue Li
This random masking essentially scales the non-peak’s synthetic read coverage according to the ratio of the gray area’s length and the non-peak’s length (when the gray area is shorter than the non-peak) so that the gray area’s synthetic read coverage mimics that of its nearby non-pe...
Data for coverage plots were generated using SAMtools depth with the -a and -Q 0 flags; a custom script then calculated the average coverage in 1 kbp nonoverlapping windows. Plots were generated using average coverage in karyoploteR.30 Southern blot of family 04 Southern blot was performed usin...
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Visualizing global satellite coverage with Planet Earlier this year Robbie Schingler, co-founder of Planet, asked Stamen to design and build a presentation that showed: Which spots on the globe Planet has daily or near-daily coverage of How this daily coverage changes during the year, due to ...
samples which contain alignments for each interval. -j output BED file with coverage of all splice-junctions in the input file. -c output BedGraph (or BigWig with '-W') file with coverage for all mapped bases. -W save coverage to -c file in BigWig format. Default output is in BED ...
especially with the wider adoption of the Nanopore PromethION sequencer. Recent developments have shown that even low-coverage long-read samples can reliably detect SVs using alignment-based SV calling83,85. However, false positives from the high sequencing error of long reads can be substantially ...
The BBC has finally lost the plot! Not content with forcibly charging a licence fee for listening and watching their stuff, you have to "log-in". What is there to log in to? I dont have a personal account with the BBC that needs protecting. I am just trying to listen / look to pu...
To validate the accuracy of the “rescued” protein isoform identifications, we used an independent multi-protease MS dataset to generate a “ground truth” of protein isoform presence, enabling us to calculate the rate of validation of the “rescued” protein isoforms within the high coverage ...
SQANTI2(4.1,https://github.com/Magdoll/SQANTI2) was used to compare the transcripts identified to the reference with parameter “-g --cage_peak --coverage --force_id_ignore.” We used the FANTOM5 cage peak dataset on hg19 and mm9 and lifted these to the hg38 and mm10 reference using...