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Hi,I've ran AA with bam file (WGS) with the code below and error message shown as follow:
AmpliconArchitect/src/AmpliconArchitect.py
--bed seed_50kb.bed
--bam pe_q0_redup.bam
--sensitivems Fal…
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For CLE, ingest will compose of two steps.
1. ~~Trim a CSV ingest file down to only samples listed that do not currently exists.~~
2. Do the actual ingest with the newly created trimmed-down list.
T…
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Hello,
I ran TRUST4 on my whole-genome sequencing data, and got the report.tsv file.
Something from the report I don't get is why some clones only have the V gene usage information and not D and J g…
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Hallo,
I have a WGS sample generated from an oral mucosa swap, sequenced with high coverage (150x) and mapped against GRCh38. Running telomerecat I get very low read values and a very low telomere …
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Thanks for the good material. I have a question about the alignment using bowtie2, here according to [`mutation_sequencing_analysis_script.sh`](https://github.com/aldob/iMUT-seq/blob/4476db76f2058d0af…
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Hello,
You had helped me get this running previously and I since adapted whole genome read detection for single transcript detection which generated some novel insights that will soon be published.…
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https://www.nature.com/articles/s41467-020-20887-6
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this c…
jjgao updated
2 years ago
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Hi,
We have constructed genomes for our 18 Mtb samples, by mapping PacBio sequencing data to the Mtb reference H37Rv using SMRT Link v 2.3.0.140936. Lineages of these samples have been experimental…
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A user suggested gramene to include sweet cherry genome. Investigate if there is a sweet cherry genome that meets Epl-Grmene inclusion criteria. ie, published, genome deposited in INSDC, gene annotati…
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Hello,
I have very low coverage (0.5-1X) whole genome sequencing data for ~200 individuals. I would like to exclude individuals based on % missing data. Is there a way to calculate missingness in…