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We observed that in the **metrics_summary.xls** file under **04.report**, the cDNA Number of reads is **1,858,750,737**, but in the **anno_decon_sorted.bam** file under the **output** directory, there…
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samtools 1.17 (using htslib 1.18)
OS: Linux 3.10.0-1160.119.1.el7.x86_64
machine architecture: x86_64
compiler: gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
#### Please specify the steps taken…
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谢谢，作者提供的强力工具，但是我在使用过程中遇到一下问题
1.使用的代码（代码在Win Rstudio中运行）
library(exomePeak2)
# library(BiocManager)
# install("BSgenome.Mmusculus.UCSC.mm10")
# library(BSgenome.Mmusculus.UCSC.mm10)
…
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My experiment consists of six samples divided in two groups. I want to carry out RiboDiPA analysis, but I got an error related with p-site mapping:
`Computing P-site offsets`
`Computing coverage…
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Hi Shian,
Thank you for the program!
I might be asking a silly question. I am currently using modkit, but I don't find a way to obtain a table that resembles your "methy" object in the user's g…
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I ran STARsolo with the `--soloFeatures GeneFull`, and I'd like to run it with `GeneFull_Ex50pAS` as well to get those statistics. Is it possible to post-process the aligned BAM file I already have? I…
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Hi,
We are looking to optimize the polishing step for reconstructing a plant genome using PacBio HiFi reads (Q30). Specifically, we tested both NextPolish and NextPolish2, followed by a variant cal…
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- [x] Remove all donwstream analyses e.g., DeSeq & PCA
- [x] change script [[count-matrix.py](http://count-matrix.py/)](http://count-matrix.py/) line 40 sep="\t" to sep = ","
- [x] switch to one s…
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Assignment instructions:
- [x] Align the reads to hg19 build 37 genome
- [x] Generate quality statistics from the fastq or bam file using your tool of choice.
- [x] Call variants for the regions in…
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Hello,
Can you clarify how to generate the rnaseq statistics using bamstats? The readme says the following:
"Provided statistics
Bamstats can currently compute the following mapping statistics:
…