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Shortstack Featured In VideoS2 - Category Vote Contest Template
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This option can increase alignment file size, sometimes by a lot. Use of this switch will cause quality values to be retained.
Note that this increases file size. Analysis Options: --bamfile [string] : path to input. Only lines with bits 4 and unset will be used.
Mutually exclusive with --readfile or --cramfile. Mutually exclusive with --readfile or --bamfile. Default: Deafult: Must be an integer of at least and no larger than 1, Note that increasing this setting may drastically increase runtimes.
Lines starting with are ignored. First column is coordinate in format Chr:start-stop, second column is names optional , and any other columns are ignored.
Mutually exclusive with option --locus. Interval s is specified in format Chr:start-stop. Multiple intervals can be specified in a comma-separated list.
Mutually exclusive with option --locifile. Must be an integer between 0 and Supply an integer between 1 and Can also be a normalized value in reads per million rpm OR reads per million mapped rpmm.
Deafult: 0. Must be a floating point number between 0. At default of 0. All others receive no strand call e.
Only stranded loci are analyzed for MIRNAs, while only unstranded loci are analyzed with respect to phasing. Most users probably want to use the default setting of 0.
Specifying this value here speeds the analysis, since ShortStack does not need to count the reads directly from the bam file. Can only be specified in conjunction with --bamfile.
At least 4G memory is suggested. Alignment and building bowtie indices tend to be the most memory-intensive portions for a given run, and memory usage seems to scale with genome size, but not as much with the number of small RNAs.
All other portions are single-threaded. At least 50G of hard disk space is recommended to be available, due to the sometimes large size of the temporary alignment files and the final alignment file.
The total time of analysis depends on several factors, including most prominently genome size, number of reads analyzed, whether or not bowtie indices need to be created, whether or not MIRNAs are being analyzed, and of course your equipment.
Specifying --readfile is mutually exclusive with both --bamfile or --cramfile Details of alignment methods and performance testing For full details on ShortStack's alignment methods and the results of performance testing, see Johnson et al.
Genome pre-processing Genome file format and naming All runs require a reference genome in FASTA format, specified with the --genomefile option.
The file must end with a valid suffix.. Within the genome, if the name of a chromosome has whitespace characters, the name will be trimmed at the first whitespace character.
This can drastically improve performance during MIRNA searching for highly fragmented genome assemblies. As of ShortStack 3. Genome indexing If not detected, an index of the genome will be created using samtools faidx.
This can be time-consuming, and memory intensive. Reads pre-processing Reads file formats Small RNA reads to be aligned must be in fasta, fastq, or csfasta formats, or their gzip-compressed versions.
File names must end with. Colorspace reads cannot be mixed with base-space reads; otherwise, mixed file formats are ok.
Color-space quality values are NOT accepted in. No paired-end support There is no support for paired-end reads in ShortStack.
No condensation Input reads are expected to be de-condensed. That is, if a small RNA was sequenced 10, times in a run, there should be 10, entries, each with a different header name, in the input readfile.
In other words, ShortStack is designed to take reads right off the sequencer without any other pre-processing except adapter trimming..
Unique read names required The small RNA reads must all have unique names within a given file. If this requirement is not met, alignments will be completely unreliable due to errors in interpreting and handling of multi-mapped reads.
Adapter trimming ShortStack has a primitive 3'-adapter capability. Specify an adapter of at least 8nts in length with option --adapter.
If nothing is given to --adapter, ShortStack assumes your reads are already trimmed. Trimming simply looks for the right-most exact match to the given apdater sequence, and when found, chops it off.
If a read is smaller than 15nts after trimming, it is discarded. For more sophisticated adapter trimming, consider cutadapt or trimmomatic If quality values are present, they are trimmed as well.
Alignment overview ShortStack uses bowtie to align reads. It first aligns, and processes the output on the fly to note how many equally good alignment positions were found for each read.
It then uses this information in a second phase to 'decide' on the most likely 'correct' location for multi-mapped reads. The final output is a single.
If multiple readfiles were input, the final bam or cram file notes the origin of each read with the RG tag see sam format specification.
This helps with sequencing errors and SNPs. If a read has some alignments with 0 mismatches, and some with 1, only those with 0 mismatches are kept.
The option --mismatches controls this threshold, and can be set to 0, 1, or 2. To get around this, when aligning to a 'large' reference, ShortStack forces the number of allowed mismatches to be 0.
The default setting is The choice of method is specified with the option --mmap. The methods are: u: Placement guided by uniquely mapping reads.
Retrieved 17 October Retrieved 17 January Retrieved 19 June The Story of Short Stack. Authority control MBA : ca64d5fcbfd22cfaef. Categories : New South Wales musical groups Musical groups established in Musical groups disestablished in establishments in Australia Universal Music Group artists.
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Wikimedia Commons. Short Stack in Budgewoi , New South Wales , Australia. Pop punk , alternative rock , pop rock. Universal Music Australia.
AUS : Gold. Homecoming  Release date: 21 August First album following reformation. AUS : Platinum. Stack Is the New Black. Sweet December EP.
This Is Bat Country. Art Vandelay. Homecoming . For Comedy Channel. Spicks and Specks. For Australian Broadcasting Corporation.
This Is Bat Country Tour . Starred in film , Co-wrote lyrics for 'Rain on her parade' and 'Die young stay pretty'. Rock Work of the Year .
Channel V Oz Artist of the Year. Calgary, Alberta T2E 5V8. Requests must be received no later than December 30, By checking that you have read the rules and regulations, You, the Sweepstakes entrant, have affirmatively reviewed, accepted, and agreed to all of the Official Rules above.
Un 1 seul prix par personne ou par foyer. Header Image. Contest Description. Entry Form. If you are randomly selected to win a shopping spree, which local participating store would you like to shop at?
I have read and agree to the terms below. Contest Rules. Your participation in the Teanaway Photo Contest helps us encourage exploration and preservation of Washington's first Community Forest.
As thanks, we've put together some great prize packages! The Scott Seymour Prize In honor of Scott Seymour, our judges will select one overall grand prize winner, who will receive:.
Scott was an avid photographer and lover of the Teanaway, who shared his perspective on Upper Kittitas County with the community for years.
His optimism and eye for beauty brightened many days. With permission from his family, we hope to encourage others to do the same.
These five first place winners will receive:. Consider these handy tips for capturing a winning photo! Pictures are powerful, and we want to ensure that the photos we feature show hiking and camping practices that set good examples for Teanaway visitors.
As a general rule, our judges will only select a if it depicts hikers staying on the trail or durable surface like snow or rock and practicing good Leave No Trace principles.
Please keep dogs on leash for photos that are entered in the photo contest. Tents should be placed on a durable surface and camps should be Leave No Trace compliant.
We want to show off your beautiful campsites and promote good backpacking and camping practices. We ask when choosing a swimming hole to be sure that it large enough to handle the impact and has an outflow.
This helps keep the ecosystem in pristine condition for the local flora and fauna, and for future hikers.
We also discourage the construction of recreational rock dams to create wading pools, as this can negatively impact fish passage and water temperature.
There are many reasons why feeding wildlife can be detrimental to them, so we ask that all photos showing wildlife be percent natural and shot from a safe and respectful distance.
If you do submit a photo of wildlife, please let us know how far away you were when it was shot! They're scenic and can make incredible focal points for catching sunrises and sunsets.
When you visit or camp in a lookout, please ensure that the lookout in question is legally open for a visit or for camping.
There are several private property parcels within the Teanaway Community Forest, and we do not want to encourage accidental trespass.
Also be sure to follow any rules that are posted at the lookout for the duration of your stay and leave the lookout in the same condition or better than you found it.
Another great opportunity to show your volunteer chops! An official entry form must be completed for each photograph submitted. The same photo cannot be entered in more than one category.
Judges reserve the right to switch images to other categories. The contest is open to all photographers, except for members of the Teanaway Community Forest Advisory Committee, contest judges and their families.
The Advisory Committee reserves the right to verify, in its sole judgment, entrant eligibility.