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Hi Sam,
Thanks for developing uncalled4 (much needed!). I am trying to obtain reference level statistics (KS comparison between two samples processed with uncalled4 align and I am running into some…
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Hi, Thanks for your software. I ran SALSA but unfortunately I didn't have satisfying result.
I applied the Arima mapping pipeline and got this statistics before SALSA:
```
perl $STATS $REP_DIR…
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Wondering if anyone has run into the following two errors. I'm running the program on 79 individuals and 6 of them are giving me one of the errors. I'm using bam files generated by LR and the followin…
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If I understood correctly, I cannot use lumpy express on a merged bam file with different RGs.
So, I have to have separate bam files (aligned with bwa mem -M -R ) and do this on each:
* Sort & I…
JJBio updated
5 years ago
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/anaconda3/envs/myenv/bin/cnvnator -root B.root -chrom chr1 -tree chr1.bam
/anaconda3/envs/myenv/bin/cnvnator -root B.root -his 1000 -fasta ucsc.hg19.fasta -chrom chr1
/anaconda3/envs/myenv/bin/cnvn…
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We will need to perform quality control on sequencing reads, `BAM` files generated by aligners and alignment statistics output by aligners.
Use the small `BAM` file provided at the following [link…
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### Description of the bug
Hi @GallVp , AssemblyQC successfully completed assessing an assembly with HiC data. When I check the HiC QC report, it mentioned [forward/reverse] Hi-C reads not found, as …
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Goal is to create a dataset that is "based on true data" but with reads on fewer genes, but with large numbers of reads per gene, so that gene-level statistics still look nice. In other words, create …
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Hi Prof. Zhu,
I tried to run my own data, but there is a error:
Make the TxDb object ... OK
Sorting and indexing BAM files with Rsamtools...[bam_sort_core] merging from 28 files and 1 in-memory…
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#### Is your feature request related to a problem? Please specify.
I'd like a simple way to calculate the coverage stats for a bam file. The closest out-of-the-box thing I can find is `samtools cov…