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Convert vcf files with phased genotypes to standard haplotype format
Convert vcf files with phased genotypes to standard haplotype format
A: Convert vcf files with phased genotypes to standard haplotype format
How to extract haplotype data from phased bcf files
How to extract haplotype data from phased bcf files
Answer: RNA-seq data for deep learning classification
Answer: Analysis of intronic reads included scRNA-seq data
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Recent Replies
Answer: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
• 0
Malat1 correlates with the intronic content and can be used as a nuclear indicator. In this preprint we discuss about this artifact and the…
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 5.9k
I wouldn't say it's true that number of reads is linearly proportional to the length of the gene. That's just an assumption that people mak…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
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Using any of the species present would likely result in a resonable annotation set. You could use *Arabidopsis* since it likely has the mos…
Comment: Downloading older version of a tool
by
GenoMax
142k
Have you tried conda install <pkg>=<version> so conda install smalt=0.5.8 <!-- junk -->
Comment: Generating mpileup file using samtools
by
Joe
21k
Older versions of software are usually available via distribution tools or the websites. It may require a lot of digging, but its almost ce…
Comment: RNA-seq data for deep learning classification
by
Yuju
• 0
Thank you very much for sharing your advice. Yes, it definitely makes sense that with the use of deep learning, models would learn normalis…
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. I can't download the older version that is menti…
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…
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