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Alexander
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Matteo Schiavinato
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Michael Love
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xqyn
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Comment: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
by
ATpoint
77k
As I said above, it depends on how you count. IGV is 1-based, BED files are 0-based, so it depends on the coordinate system. On the molecul…
Answer: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
by
suragnair
•
0
Turns out +4/-4 is the correct shift. You can see that when you make a bigwig separately from the + and - strands, then the reads align wit…
Answer: ATAC-seq +4 -5 shift
by
suragnair
•
0
Turns out +4/-4 is the correct shift. You can see that when you make a bigwig separately from the + and - strands, then the reads align wit…
Answer: Assessing Rockhopper's output
by
shelkmike
▴
980
I didn't do *de novo* transcriptome assemblies with Rockhopper. Only reference-based analyses. However, having very long transcripts is nor…
Answer: Recommendations for extending contigs from denovo assembly to identify SV insert
by
shelkmike
▴
980
Some time ago I made a tool Elloreas (https://github.com/shelkmike/Elloreas) that iteratively extends a contig using long reads. It can be …
Answer: How to get the gft file to run velocyto for velocity analysis?
by
ATpoint
77k
You need the same GTF file that was used during mapping of your 10x data. If you used CellRanger and it was mouse (given you used recent Ce…
Answer: Lower alignment rate when using collapsed reads
by
LChart
3.4k
Sequences are collapsed if they're sufficiently identical. Garbage (random) reads won't collapse. If you collapse the "good" reads and don'…
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
LChart
3.4k
(1) Yes; but you can simply subset the DESeq via `dds[,dds$donor != UNWANTED_DONOR]`
(3) Given the initial results (and the MDS) that dono…
Answer: Unmapped Reads in Kallisto
by
dsull
★
4.7k
Running kallisto bus with the -n option will record the read numbers of the reads that have been successfully mapped in the output BUS file…
Comment: Automate the Splitting of a VCF File by Sample (bcftools)
by
cfos4698
▴
830
Just a comment re: your bash example reading from a file. Have you tried `while` instead of 'with'?
```
while read sample; do
bcftools…
Comment: Split plink files by a number of SNPs
by
Raygozak
★
1.4k
Out of curiosity, why would someone ask how to do something if they already knew how to do it or which tools to use?
Also, the OP is not a…
Comment: Comparing multiple RNASeq studies
by
Zhenyu Zhang
▴
980
no.
The best you can do is to draw conclusion using one dataset, and validate your conclusion using other datasets.
Comment: comparision of umap single cell
by
synat.keam
▴
80
Thank, Seniors.. I figured out the issue of my integration as I did not state the ``` reduction= "harmony" ```
Comment: Issue with merging in plink and eigensoft.
by
bk11
★
1.2k
> I merged two datasets in plink1.9. It worked, but I did get the error
> "multiple positions seen for variant" and "variants have the same…
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