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Recent Replies
Comment: [SOLVED] How to build a table with gene expression per cell type with Seurat ?
by
oomoru
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0
Thanks Evan!
Gene_Count_Per_Cell.tsv, first barcode- 1_AAACCTGAGACTTGAA.1
Convert_UMI_Label.tsv, first barcode- 1_AAACCTGAGACTTGAA.1
…
Comment: How do you limit the result from the BLAST executable?
by
gb
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This question was already answered. You have to do a few steps before blasting. Because you did a PCR you have many duplicate sequences as …
Comment: Protein homolog query issue
by
Jean-Karim Heriche
24k
If the genome is available but poorly annotated, I don't see how you can avoid getting better annotations. Try with exonerate.
Answer: Mark Duplicates
by
toralmanvar
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940
You need to use .bam file as input and not the bam index. i.e your command should be:
java -jar $EBROOTPICARD/picard.jar MarkDuplic…
Comment: Single-stranded RNA-seq: strandedness of samples
by
fr
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160
@atpoint thank you very very much, I really appreciate it. You are correct, the instrument is Nextset500, not 5000.
I can see now that …
Comment: Visualiation of samtools depth output in a plot
by
dominik.lagler
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10
thanks was very helpful;)
Comment: [SOLVED] How to build a table with gene expression per cell type with Seurat ?
by
Evan
▴
120
Hi, it seems the cells abels in the file "Convert_UMI_Label.tsv" are not the same than in the raw counts matrix "Gene_Count_Per_Cell.tsv". …
Comment: Why is WGS/WES depth of Y chromosome highly variable?
by
German.M.Demidov
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2.3k
tbh I do work with exomes/genomes a lot and I wrote a CNV caller which infers sex based on X/Y ratio ( https://github.com/imgag/ClinCNV ) -…
Comment: Postdoctoral Position, Department of Biology , Colorado State University
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Jean-Karim Heriche
24k
Edited the post title to also show location.
Comment: Considering the multiple test correction for the analysis of polygenic risk scor
by
German.M.Demidov
★
2.3k
Correlations between SNPs are not corrected via multiple testing correction, but by LD prunning or clumping.
https://www.biostars.org/p/3…
Comment: [SOLVED] How to build a table with gene expression per cell type with Seurat ?
by
oomoru
•
0
Thank you very much, this is so helpful to me. I used to the code but had error with this section-
---------------------------------------…
Answer: TypeError: must be real number, not dict in python
by
sbstevenlee
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140
Is this what you are currently doing?
```
>>> import math
>>> d = {'a': 1, 'b': 10, 'c': 100}
>>> math.log10(d)
Traceback (most rece…
Answer: What cut-offs to use for Genomic Features Pie Chart for Methylation Array Data?
by
Papyrus
★
1.1k
I my experience the classification as "unmethylated" and "fully methylated" is completely arbitrary. You could look at the histogram of b-v…
Answer: How many reads does Delly use for variant calling?
by
trausch
★
1.6k
It uses the entire BAM file and requires at least 2 paired-ends or split-reads to call a variant.
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