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Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
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Recent Replies
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
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thanks, it's working now.
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@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
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Trivas
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You need to have indexed your bam/sam file using `samtools index`
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The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
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According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
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There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2]
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Hi, I emailed them and did get the bed file! Thank you so much.
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1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
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You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
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ntsopoul
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does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
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Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
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![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
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I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
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