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Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 26 days ago by 41k • written 10.1 years ago by ★ 7.8k
48
votes
30
replies
9.3k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 28 days ago by 78k • written 7.7 years ago by 41k
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 22 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
19
votes
13
replies
7.9k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 26 days ago by • 0 • written 17 months ago by 78k
0
votes
4
replies
437
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
18 days ago by Coremine Medical ▴ 20
2
votes
0
replies
933
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 15 days ago by • 0 • written 10 months ago by ★ 1.6k
0
votes
0
replies
236
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
24 days ago by rohitsatyam102 ▴ 780
5
votes
0
replies
4.2k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
21 days ago by GenoMax 136k
0
votes
0
replies
163
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
3 days ago by rohitsatyam102 ▴ 780
1
vote
0
replies
589
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 22 days ago by 41k • written 8 months ago by ▴ 10
10 results • Page 1 of 1
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Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
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Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads by cee28 • 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by DINESHR • 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by dsull ★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM? by rpolicastro 12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks by Ankit ▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by cmdcolin ★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by rpolicastro 12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file by ATpoint 78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
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