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Review of: Shortstack

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On 12.05.2020
Last modified:12.05.2020


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Erhalte detaillierte Informationen über ShortStack zu Benutzerfreundlichkeit, Funktionen, Preis, Vor- und Nachteilen aus verifizierten Nutzererfahrungen. Englisch-Deutsch-Übersetzungen für short stack im Online-Wörterbuch synthetikpark.com (​Deutschwörterbuch). ShortStack. Gefällt Mal · 13 Personen sprechen darüber. https://www.​synthetikpark.com Use ShortStack to build contests, sweepstakes, data-collection.


Erhalte detaillierte Informationen über ShortStack zu Benutzerfreundlichkeit, Funktionen, Preis, Vor- und Nachteilen aus verifizierten Nutzererfahrungen. Teilnahmebedingungen für das Facebook Gewinnspiel. DÖRFLER Leder & Mehr​, Montag, T. Das Gewinnspiel steht in keiner Verbindung zu. Englisch-Deutsch-Übersetzungen für short stack im Online-Wörterbuch synthetikpark.com (​Deutschwörterbuch).

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Eine Barauszahlung oder ein Tausch der Gewinne sind ausgeschlossen.

Best For Small businesses, enterprise-level businesses and agencies use ShortStack to build tailored, engaging and shareable campaigns - contests, sweepstakes, forms, landing pages, promotions, quizzes, etc.

Founded in Located in United States. Starting Price. Yes, get a free trial. ShortStack Features. Skills Contests Photo, Essay, Design, etc.

Landing Page. Lead Capture. Marketing Automation. ShortStack Alternatives. Award Force. OpenWater Software. Rewards Fuel. Compare with Similar Products.

Current Product ShortStack. Add to Compare. Awards management software for leading awards organisers to manage entry and judging online.

Fast, secure and a great experience Spinify is for organisations who are serious about contest and gamification; we help companies reach their goals and change culture.

Powerful contest management software to boost your brand. 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.

During the alignment, the count of uniquely mapped reads is kept in 50nt bins across the reference genome. The bin location is determined by the left-most coordinate of the uniquely mapped read.

After the first phase of alignment for all reads in all files has completed, this genome-wide map of uniquely-mapped read counts is used to guide the decisions of the most likely locations of multi-mapped reads.

Specifically, for a given multi-mapped read, the local count of uniquely mapped reads at each possible location is computed.

The local count is that of the specific 50nt bin the alignment lies in again, by left-most positon plus the counts of the 2 bins upstream and 2 bins downstream.

All of the local counts are converted to fractions of the sum of all total counts. These fractions are then used as the probabilities of placement for the multi-mapped read.

For instance, suppose a multi-mapped read had three possible positions. The read counts of uniquely mapped reads were 30, 65, and 5. The actual choice is probabilistic, given the computed weightings, for each read.

Like u, except that multi-mapped reads also contribute to the guidance densities. This is faster than u and f, but performs much more poorly at properly placing multi-mapped reads.

Achieves high sensitivity, but very low precision. Very fast, but ignores large quantities of data. Achieves high precision, but very low sensitivity.

The default setting for --mmap is u ranmax When running mmap method u or f, there are some cases where no guidance can be given, and so the choice on where to put a multi-mapped read is still random.

In those cases, the option ranmax will suppress any alignment where the choice is 'too' random. May September MTV Australia.

Nova FM. Channel 5. Retrieved 28 October Retrieved 14 April Retrieved 17 December Retrieved 10 February Archived from the original on 6 May Australian Recording Industry Association.

Archived from the original on 27 September Retrieved 2 October 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.

Namespaces Article Talk. Views Read Edit View history. Help Learn to edit Community portal Recent changes Upload file. Download as PDF Printable version.

Wikimedia Commons. All entries become the permanent property of the Sponsor s and none will be returned. This Sweepstakes is void where prohibited by law and is subject to all applicable federal, provincial and municipal laws.

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1 Kommentar

  1. Zuluzragore

    Ich entschuldige mich, aber diese Variante kommt mir nicht heran.

  2. Faerr

    Es ist der Fehler geschehen

  3. Yoshicage

    Eindeutig, die ausgezeichnete Antwort

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