umis | Tools for processing UMI RNA-tag data | Genomics library
kandi X-RAY | umis Summary
kandi X-RAY | umis Summary
umis provides tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias. There are four steps in this process.
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Top functions reviewed by kandi - BETA
- Compute the tagcount for each evidence
- Guess the cutoff depth cutoff from the barcode distribution
- Return a stream of samples from a BAM file
- Read a CWL file
- Demultiplex a fastq file
- Return set of fastq annotations in a fastq file
- Construct a regular expression based on annotations
- Make a directory
- Transforms fastq files
- Extract the readnum from a read dict
- Read a fastq file
- Infer transform options
- Run kallisto
- Return a set of all cellular barcodes in the given histogram
- Extract tags from a BAM file
- Return a set of annotations in the query alignment
- Filter UMI files according to UMIs
- Generate mutation hash dictionary
- Add ids to uids
- Count the number of reads in a fastq file
- Filter fastq files using samtools
- Calculate the CBB histogram for a fastq file
- Sub subset of bam file
- Filter fastq files
- Demultiplex cells
- Perform a fasttag count
umis Key Features
umis Examples and Code Snippets
Community Discussions
Trending Discussions on umis
QUESTION
I'm writing some code to de-duplicate data based on 2 fields:
- A string of characters, we'll call this the UMI
- An array of integers
I've created a POJO to hold this data and work as key for a TreeMap. The full set of data is held in the value - this way I only keep relevant data in memory.
However, the next requirement is to have variability in the UMI AND the integers. For example, the following two pieces of data would be considered duplicates based on the UMI having a variability(mismatch) of 1.
a. "AAA", [200,300]
b. "ABA", [200,300]
Similarly, the following would be considered duplicates based on the integer array, given a mismatch allowance of 2.
a. "AAA", [201,300]
b. "AAA", [203,300]
My current attempt has been to make this POJO implement the Comparable interface, and attempt to work the compareTo method to take into account the variability:
ANSWER
Answered 2019-Jan-07 at 13:24According to the docs of compareTo:
The implementor must ensure sgn(x.compareTo(y)) == -sgn(y.compareTo(x)) for all x and y. (This implies that x.compareTo(y) must throw an exception iff y.compareTo(x) throws an exception.)
The implementor must also ensure that the relation is transitive: (x.compareTo(y)>0 && y.compareTo(z)>0) implies x.compareTo(z)>0.
Finally, the implementor must ensure that x.compareTo(y)==0 implies that sgn(x.compareTo(z)) == sgn(y.compareTo(z)), for all z.
I think that's not true to your code, and that could cause problems with the get function not finding your entry
QUESTION
ANSWER
Answered 2018-Dec-16 at 14:56Use double quotes for the nested fields
QUESTION
This is literaly driving me crazy!!!
I have a php page that generates an HTML file, in which there are some javascript functions that trigger some selects and other stuff. One of these JSs generates also a field that is meant to be a date, in which I want to use Bootstrap Datepicker plugin. I can't make it work and I don't know why, since in other pages including the same CSSs and JSs it works perfectly...so, what's my mistake in this page?? Please help!
...ANSWER
Answered 2017-May-10 at 10:00In your case, the relevant events are added to the select at the wrong time: Try this:
QUESTION
This might sound very strange and probably it is, so forgive me if I'm committing a bad mistake.
I have an unspecified number of , generated at runtime and identified with a progress number id like id='data1', id='data2'...I would like to have a jQuery script on every input. I thought to generate x scripts for x inputs but it doesn't work.
How could I do this?
...ANSWER
Answered 2017-Mar-15 at 15:11Use attribute selector [] with the start with ^ selector ([id^="data"]), your code should be :
QUESTION
I'm developing a web-app and I'm always getting this problem: often I have to generate some HTML code via Javascript (for example a user selects the number "6" in a select and I generate 6 fields via JS). The problem is that I can't understand how to link jQuery (or Javascript) functions to those Javascript-generated fields because all the classical methods don't seem to work. In this case I want that my user will only be allowed to type the numbers 0-9 and the backspace, so I wrote this simple jQuery function:
...ANSWER
Answered 2017-Mar-15 at 09:54if you generate html on the fly you should use
QUESTION
I have a grid view that has a column containing strings (Middle column).
On the rowDataBound event I want to loop through the column looking for the integer it contains and then display a value in the first column.
I know that the integer range will be 1 to 63 so I can use a FOR loop to loop through the numbers. Here is what I have so far.
ANSWER
Answered 2017-Feb-21 at 14:54Go backwards in a Do Until Loop:
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Install umis
You can use umis like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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