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Answer: Analysis of intronic reads included scRNA-seq data
Answer: Controlling for FDR in 450k methylation microarray data
Comment: Generating mpileup file using samtools
Comment: Generating mpileup file using samtools
Answer: Downsampling long-read BAM files
Comment: Generating mpileup file using samtools
Answer: What analysis suitable to identify similarly expressed genes between two samples
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Recent Replies
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
Comment: read length in structural variant calling
by
eebloom
▴ 80
Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I just realised I didn't align my reads with the tools they used and used bowtie2 instead. The tool isn't available on conda and I can't fi…
Comment: Downsampling long-read BAM files
by
eebloom
▴ 80
This is not what I needed for this particular use case, as capping the coverage would lose the information on regions of copy number amplif…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Apologies, I deleted the question as I wasn't sure it would be helpful to others and it didn't seem to have a clear answer, not to snub the…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Thanks, I think it would be a good idea to track the results downstream to look for batch effects. I think I will filter the reads ultimate…
Comment: Generating mpileup file using samtools
by
ATpoint
82k
Seconding this. Apply current best practices (which is bcftools mpileup followed by something I forgot, see bcftools manual for variant cal…
Answer: Analysis of intronic reads included scRNA-seq data
by
ATpoint
82k
By default in CellRanger (lets assume you have 10x data processed with it) intronic reads are included. What you get in your matrix.mtx fil…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
The number of reads for a gene is almost exactly linearly proportional to the length of the gene. In paired-end sequencing, we generally co…
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
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