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912

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Using needle command with no output to the terminal

silent needle emboss written 2.5 years ago by Jacob • 10 • updated 2.5 years ago by Charles Plessy • 2.7k

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994

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cbioPortal MutationMapper protein domain annotation not up-to-date

lollipop needle written 3.3 years ago by Nicolas Rosewick ♦ 8.6k • updated 3.2 years ago by Biostar ♦♦ 20

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1.3k

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Needle Crashing on Specific Sequences

pairwise fasta needle alignment emboss written 3.5 years ago by juanfelipe2005 • 10 • updated 3.5 years ago by 5heikki ♦ 8.6k

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2.9k

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EMBOSS Needle: Read sequences from stdin

linux needle stdin unix emboss written 5.7 years ago by pld ♦ 4.8k • updated 5.7 years ago by brentp ♦ 23k

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Recent Replies

A: ABySS Bloom filter false positive rate by metageni • 60
Looks a like a question for https://github.com/bcgsc/abyss/issues
C: PCA vs ICA prior to t-SNE or UMAP by CY • 460
> the only relevant components to explain the variability in the data are the uncorrelated one...
C: How to plot 2 different symbols in a 3D PCA plot generated by rgl-plot3D by maria2019 • 80
True! thanks for your comment. I just tried it. The problem with plot3D is that I cannot rotate t...
A: Design matrix for voom: with or without batch blocking? by Gordon Smyth • 1.3k
See Chapter 15 (RNA-seq Data) in the limma User's Guide. The comments there apply to proteomics c...
A: limma voom problem by Gordon Smyth • 1.3k
The design matrix needs to have fewer columns than rows, preferably much fewer columns than rows....
C: Event-based software for alternative splicing with three conditions? by Jeremy Leipzig ♦ 18k
i'm not so sure software that handles 3 conditions is really much better than A vs B and A vs C a...
C: Fast download of FASTQ files from the European Nucleotide Archive (ENA) by jcmcnch • 0
Amazing! Thank you so much Ben - your script "just works"! Now instead of variable download speed...
C: issues using Value Matching command in R by Fabio Marroni • 2.4k
tab[tab[,1]=="ENSG00000223972.4",] You have to check that the first column is of character t...
C: How to plot 2 different symbols in a 3D PCA plot generated by rgl-plot3D by mbk0asis • 500
I think 'plot3D' and 'plot3d' are different. Former one is a package, while the later is a function.
C: Looking for the soft that generated this figure by mbk0asis • 500
I'm not sure there is a software for such plots, but I think geom_point (ggplot2) can do the job ...
A: Extracting Multiple Mapped reads from Bismark output by metageni • 60
I'm not familiar with `Bismark `, but [here it says][1] that the output can be in BAM format. If...
C: only unique mapped paired-end reads by Ric • 290
In the first or second `samtools view` command?

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