Gray Man" benutzt der Charakter Kanda immer wieder herablassend das Wort "Shortstack", wenn er seinen Teamkollegen Walker anspricht. Teilnahmebedingungen für das Facebook Gewinnspiel. DÖRFLER Leder & Mehr, Montag, T. Das Gewinnspiel steht in keiner Verbindung zu. The short stack in the big blind makes the gap small. Der Shortstack im Big Blind macht den 'Gap' kleiner.
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Shortstack Featured In VideoS2 - Category Vote Contest Template
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However, that templated framework has its limits, keeping you from realizing fully customized ideas outside that framework.
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Cat 5 Vote Text. Requirements for input bam or cram files: 1. Header must be present, and contain SQ lines. File most be sorted.
Read groups will not be recognized unless they are properly noted in the header. Paired-end, spliced, clipped, padded, or gapped alignments will be ignored, with a warning to the user.
Reads marked as secondary alignments bit set in the FLAG will not be used. The mincov threshold can also be specified in terms of reads per million by using a value such as 3.
Using a rpm threshold allows the sensitivity of cluster discovery to be normalized between libraries of different sizes. Alternatively, reads per million mapped rpmm can be specified: A --mincov of 1.
Only small RNAs with an abundance higher than the limit set by option --mincov are reported. These small RNAs typically inlcude RNAs that could not be aligned anywhere on the reference, as well as multi-mapped RNAs where ShortStack did not choose a alignment position for see alignment methods.
For just one or a few loci, the option --locus can be used. The argument should be a coordinate in the format Chr:Start-Stop.
Multiple loci can be specified in option --locus by using commas to delimit them. For larger lists of user-defined loci, and external file can be used instead, specified with option --locifile.
The file is a plain-text , tab-delimited format. The first column should list the coordinates in Chr:Start-Stop format. An optional second column can contain names of the loci.
Any other columns will be ignored. Also, lines starting with will be ignored. Options --locus and --locifile are mutually exclusive.
Also, if either is used, no de- novo cluster finding occurs. The major methods are described below: Read-group-specific counts Quantification occurs separately for each read-group in the alignment.
The results are in the 'Counts. When there are multiple read-groups, this is helpful to gather the raw data for differential expression analysis.
There is always a read-group called 'main', which is all read-groups combined. All other loci are given a strand of. Note that the predominant RNA size need not be a majority..
It therefore probably allows some degree of false negatives e. If a locus fails a certain step, it is removed from consideration and given a specific code indicate what step it failed.
The codes are below in step-wise order. Increasing this size may allow you to find more MIRNAs, but will also slow down the runtime of the process.
N3: Major RNA abundance was less than 2 reads. N General failure to compute miRNA-star position if occurs, possible bug? N Maybe. Y: Yes. Can support a de novo annotation of a new miRNA family.
MIRNA analysis can be disabled with the --nohp option. This may save significant analysis time. As of ShortStack version 3.
Phasing Phasing here refers to a signature of periodicity of small RNA abundance that reflects dsRNA processing from a defined terminus.
For valid loci, ShortStack 3. ShortStack calculates the phase score in a 21 nt phase size for loci with a DicerCall of 21, or in a 24 nt phase size for loci with a DicerCall of 24, and returns the score.
Higher phasing scores indicate more phasing signature. Phase scores range from very near 0 worst up. The modification of the Guo et al.
Not all loci are subject to phasing analysis. These are assigned a PhaseScore of Log file A log of the run messages is created and written to Log. ErrorLogs For debugging.
Most users won't need to look at this. It stores the verbose outputs of bowtie-build, bowtie, samtools sort, and samtools merge commands that are not kep in the main Log.
Sometimes these are helpful in diagnosing bugs, particularly samtools sort and merge bugs due to memory issues. Stitched genome file If the input genome was 'stitched' see above , the stitched genome file will be put in the ShortStack outdir, along with its fai index temporarily during the run.
Both files will be deleted at the end of the run so you won't see them unless your run was killed before completion for some reason.
Results file The file Results. The columns are labeled in the first row, and are: 1. Locus: Coordinates of the locus in format Chr:Start-Stop 2.
Name: Name of the locus 3. Length: Length of the locus nts 4. Reads: Total number of primary alignments in the locus 5.
RPM: Total number of primary alignments normalized to reads per million. Note the the normalization factor includes all primary alignments..
UniqueReads: Number of uniquely aligned primary alignments in locus. FracTop: Fraction of primary alignments aligned to the top genomic strand 8.
Strand: Strand call for the locus 9. In cases of tie, MajorRNA is arbitrarily chosen from the tied entries.
Lower numbers indicate loci that are more dominated by a single highly abundant RNA. Can also be NA if the locus had no aligned reads.
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