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Tool: Aquaria: simplifying discovery and insight from protein structures

snp tool sequence aquaria 3d structure written 5.0 years ago by Aquaria team • 90

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Recent Replies

A: Ambiguous fields in FANTOM 5 Enhancer_TSS_association.bed file by Corentin • 430
Hi, The file is in the BED12 format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 . This fo...
C: Is it possible to remove reads from BAM which match the reference at a position by yryan • 0
That worked perfectly, thanks so much for that!
C: Possible reasons mapping percentage abysmally low for miRNA reads? by genomax ♦ 76k
It is certainly possible that you have bad/less than optimal data. If you get a similar result wi...
C: Google Summer of Code 2020 announced for mentor organisations by Emily_Ensembl ♦ 20k
Mentor applications are now open and will be open until 5th February.
C: Possible reasons mapping percentage abysmally low for miRNA reads? by Cookie-san • 40
So you think the problem is with the aligner and not the data? I will try bbmap.sh as you suggest...
C: Possible reasons mapping percentage abysmally low for miRNA reads? by genomax ♦ 76k
If you are willing to try a different aligner then you could try using `bbmap.sh` with these para...
C: Case control status permutation in GWAS by German.M.Demidov • 1.2k
Aren't you supposed to calculate p-values from the permuted data? And then just use Manhattan plot?
C: GATK HaplotypeCaller/GenotypeGVCFs assigning GQ 0 and GT ./. at well-covered, hi by Dataman • 310
I have also recently encountered this problem. Did you find out the answer to your question? It s...
C: Possible reasons mapping percentage abysmally low for miRNA reads? by Cookie-san • 40
mapper.pl from miRDeep2 uses bowtie (1). Seed length is 18bp, and it allows no mismatch in this a...
C: Possible reasons mapping percentage abysmally low for miRNA reads? by genomax ♦ 76k
What aligner are you using? Is it doing ungapped alignments as would be needed for reads ~18 bp?
A: Is it possible to download nr db from NCBI's cloud ? by genomax ♦ 76k
Database files available on NCBI's FTP site are always current. You don't want to download the fa...
C: DE genes and variability between biological replicates: edgeR by genomax ♦ 76k
https://www.biostars.org/u/38076/ : Please use `ADD COMMENT/ADD REPLY` when responding to existin...

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