All Site Activity
Neel commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites- Neel bookmarked ASCIIGenome: genome browser based on command line interface and designed for running from console...Comments
- Jit 1723 days ago
This a list of available commands with their brief description.
For help on individual commands use one of::
command -h
?command
help command
e.g. `ylim -h`
N a v i g a t i o n
goto chrom:[from]-[to]
Go to region `chrom:from-to` or to `chrom:from` or to the start of
`chrom`.
INT from [c | to]
Go to position `from` or to region `from to` on current chromosome.
PERCENT from [c | to]
Zoom into the current window delimited by given PERCENT of screen.
+ INT [k|m]
Move forward by `INT` bases. Suffix K/M recognized.
- INT [k|m]
Move backwards by INT bases. Suffix K/M recognized.
f [NUM=0.1]
Move forward NUM times the size of the current window, 1/10 by default.
b [NUM=0.1]
Move backward NUM times the size of the current window, 1/10 by default
ff
Move forward by 1/2 of a window. A shortcut for `f 0.5`
bb
Move backward by 1/2 of a window. A shortcut for `b 0.5`
zi [INT = 1]
Zoom in INT times. Each zoom halves the window size.
zo [INT = 1]
Zoom out INT times. Each zoom doubles the window size.
extend [mid|window] [INT left] [INT right]
Extend the current window by `INT` bases left and right.
l
Go to the Left half of the current window.
r
Go to the Right half of the current window.
p
Go to the previous visited position.
n
Go to the next visited position.
next [-back] [-start] [-zo INT=5] [track]
Move to the next feature not overlapping the current coordinates.
F i n d
find [-all] [-c] [-F] regex [track]
Find the first record in `track` containing `regex`.
seqRegex [-iupac] [-c] [regex]
Find regex in reference sequence and show matches as an additional
track.
bookmark [-d] [-n name] [-print] [> file] [chrom:from-to]
Creates a track to save positions of interest.
D i s p l a y
grep [-i = .*] [-e = ''] [-c] [-F] [-v] [track_regex = .*]...
Similar to grep command, filter for features including or excluding
patterns.
awk [-off ...] [-F sep_re] [-v VAR=var] [-V] '<script>' [track_regex = .*]...
Advanced feature filtering using awk syntax.
featureColorForRegex [-r/-R regex color] [-v] [track_regex = .*]...
Set colour for features captured by regex.
featureDisplayMode [-expanded | -collapsed | -oneline] [-v] [track_regex = .*]...
Set how annotation features should be displayed.
gap [-on | -off] [-v] [track_regex = .*]...
Display features with or without a separating gap.
gffNameAttr [attribute_name = NULL | -na] [-v] [track_regex = .*]...
GTF/GFF attribute to set the feature name or `-na` to suppress name.
trackHeight [-v] INT [track_regex = .*]...
Set track height to INT lines of text for all tracks matching regexes.
ylim [-v] <NUM|min|na> <NUM|min|na> [track_regex = .*]...
Set the y-axis limit for all tracks matched by regexes.
colorTrack [-v] color [track_regex = .*]...
Set colour for tracks matched by regex.
hideTitle [-on | -off] [-v] [track_regex = .*]...
Set the display of the title line matched by track_regex.
genotype [-n 10] [-s .*] [-r pattern rplc] [-f expr] [-v] [track_regex = .*]...
Customise the genotype rows printed under the VCF tracks.
editNames [-t] [-v] <pattern> <replacement> [track_re=.*]...
Edit track names by substituting regex pattern with replacement.
dataCol [-v] [index = 4] [track_regex = .*]...
Select data column for bedgraph tracks containing regex.
print [-n INT] [-full] [-off] [-round INT] [-hl re] [-esf] [-v] [-sys CMD] [track_regex = .*]... [>|>> file]
Print lines for the tracks matched by `track_regex`.
A l i g n m e n t s
readsAsPairs [-on | -off] [-v] [track_regex = .*]...
Show SAM records as pairs.
filterVariantReads [-r from/to] [-all] [-v] [track_regex = .*]...
Filter reads containing a variant in the given interval.
rpm [-on | -off] [-v] [track_regex = .*]
Set display to reads per million for BAM and TDF files.
samtools [-f INT=0] [-F INT=4] [-q INT=0] [-v] [track_re = .*] ...
Apply samtools filters to alignment tracks captured by the list of
track regexes.
BSseq [-on | -off] [-v] [track_regex = .*]...
Set bisulfite mode for read tracks matched by regex.
G e n e r a l
setGenome fasta|bam|genome
Set genome and reference sequence.
setConfig <file|tag> | <key> <value>
Set configuration arguments.
explainSamFlag INT [INT ...]
Explain the list of bitwise SAM flags.
show <arg>
Show or set features to display.
recentlyOpened [-grep = .*]
List recently opened files.   - Rahul Nayak 1723 days ago
Install ASCIIGenome with conda
(base) [wsu29@bladeamd-2 ~]$ conda install ASCIIGenome
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /data/sata_data/workshop/wsu29/miniconda3
added / updated specs:
- asciigenome
The following packages will be downloaded:
package | build
---------------------------|-----------------
asciigenome-1.15.0 | 0 27.5 MB bioconda
openjdk-8.0.152 | h7b6447c_3 57.4 MB
------------------------------------------------------------
Total: 84.9 MB
The following NEW packages will be INSTALLED:
asciigenome bioconda/noarch::asciigenome-1.15.0-0
openjdk pkgs/main/linux-64::openjdk-8.0.152-h7b6447c_3
Proceed ([y]/n)? y
Downloading and Extracting Packages
openjdk-8.0.152 | 57.4 MB | ################################################################################### | 100%
asciigenome-1.15.0 | 27.5 MB | ################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
- Neel created a new bio-script CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
- Neel created a new bio-script Script to Plot the Coverage
- Neel created a new bio-script Collecting arguments with R
- Abhimanyu Singh posted to the wire
- Rahul Nayak posted to the wire
- Jit bookmarked Referee: Genome assembly quality scores
- Rahul Nayak published a news post Illumina to Acquire Pacific Biosciences for Approximately $1.2 Billion !
