Bow tie map file

Things seem to have reached the point where there is mainly a trade-off between speed, accuracy, and configurability among read mappers that have remained popular. There are over 50 read mapping programs listed here. Each mapper has its own set of limitations on the lengths of reads it accepts, on how it outputs read alignments, on how many mismatches there can be, on whether it produces gapped alignments, on whether it supports SOLiD colorspace data, etc.

As evidence of how things are settling down, we're going to just use bowtie2 in this course. Previous versions of this class and tutorial have covered using bowtie and bwa. Please consult these tutorials for more specific information on each mapping program. Last year's tutorial included a trimmed down version of the bwa tutorial.

Please see the Introduction to mapping presentation for more details of the theory behind read mapping algorithms and critical considerations for using these tools correctly. They are Illumina Genome Analyzer sequencing of a paired-end library from a haploid E.

The reference genome is the ancestor of this E. See if you can figure out how to do that. When you're in the right place, you should get output like this from the ls command.

Often you will have general questions about your sequencing files that you want to answer before or after starting your actual analysis. Here we show you some very handy commands after a warning:. NGS data can be quite large, a single lane of an Illumina Hi-Seq run generates 2 files each with s of millions of lines.

Printing all of that can take an enormous amount of time and may crash your terminal long before it finishes. Below are several commands we've already been using, and some new ones put together to improve your skills.

Occasionally you might download a sequence or have it emailed to you by a collaborator in one format, and then the program that you want to use demands that it be in another format.

Why do they have to be so picky? So, we've put it in a place that you can run it from for your convenience. However, remember that any time that you use the script you must have the bioperl module loaded. Remember, those are your "base quality scores". Many mappers will use the base quality scores to improve how the reads are aligned by not placing as much emphasis on poor bases.

Bowtie2 is a complete rewrite of bowtie. After years of teaching bwa mapping along with bowtie2, we've decided that you will be the first class to use only bowtie2 since we never recommend anyone use bwa.

For some more details about the differences between them see the bonus presentation , and if you find a compelling reason to use bwa rather than bowtie2, we'd love to hear from you. Create a fresh output directory named bowtie2. We are going to create a specific output directory for the bowtie2 mapper within the directory that has the input files so that you can compare the results of other mappers if you choose to do the other tutorials. Remember in our earlier tutorial we discussed the use of lonestar's module commands "spider" and "load" to install new functionality.

Note that which can be very useful for making sure you are running the executable that you think you are running, especially if you install your own programs. In particular make sure that the path matches up to what you expect. Generally speaking, the first step in mapping is quite often indexing the reference file regardless of what mapping program is used. Put the output of this command into the bowtie directory we created a minute ago.

The command you need is:. Try typing this alone in the terminal and figuring out what to do from the help show just from typing the command by itself. The command requires 2 arguments. The second argument is the "base" file name to use for the created index files. Short reads to align to the indexed reference, specified as a character vector, string, string vector, or cell array of character vectors indicating one or more FASTQ formatted files with the input reads.

Name for output file containing the results of the short read alignment, specified as a character vector or string. By default, the output file is BAM-formatted, and bowtie automatically adds the.

In this case, bowtie automatically adds the. Specify optional comma-separated pairs of Name,Value arguments. Name is the argument name and Value is the corresponding value. Name must appear inside quotes.

You can specify several name and value pair arguments in any order as Name1,Value1, Indicator for the output file format, specified as the comma-separated pair consisting of 'BamFileOutput' and either true or false. If true the default , then the output file is BAM-formatted, with a. If false , then the output file is SAM-formatted, with a. Example: 'BamFileOutput',false.

Indicator for paired-read alignment performance, specified as the comma-separated pair consisting of 'Paired' and either true or false the default. If false , then bowtie performs paired-read alignment using the odd elements in reads as the upstream mates and the even elements in reads as the downstream mates. Example: 'Paired',true.

You can force them to appear in the same order at a slight cost in speed by adding the --reorder flag to your command, but is typically only necessary if the reads are already ordered or you intend to do some comparison between the input and output. In the bowtie2 example, we mapped in --local mode. Try mapping in --end-to-end mode aka global mode. The next steps are often to view the output using a specific viewer on your local machine, or to begin identifying variant locations where the reads differ from the reference sequence.

These will be the next things we cover in the course. Here is a link to help you return to the GVA course schedule. Pages Blog. Space shortcuts File lists How-to articles. Page tree. Browse pages. A t tachments 0 Page History. Hide Inline Comments. Jira links. Created by Daniel Edward Deatherage , last modified on May 27, Other read mappers Previous versions of this class and tutorial have covered using bowtie and bwa. If you need a little help but don't want the answer yet, click the triangle Remember that to copy an entire folder requires the use of the recursive -r option.

Still stuck? Beware the cat command when working with NGS data NGS data can be quite large, a single lane of an Illumina Hi-Seq run generates 2 files each with s of millions of lines. How to count the total number of lines in a file Expand source. How to determine the total number of sequences in a fastq file Expand source.

How to determine how long the reads are in a fastq file Expand source. Click here for a hint. Expand source. Use of uninitialized value in concatenation. Click here if you need a hint. Click here for the answer Expand source. Commands for making a directory and changing into it Expand source. Click here for a hint without the answer. Remember in our earlier tutorial we discussed the use of lonestar's module commands "spider" and "load" to install new functionality click here for the answer without having to go back through the previous tutorial Expand source.

Here are a few of the possibilities that will work. In this case all of these methods will work, that may not be true of all programs. If you're stuck and want a hint without the answer If you're stuck click here for an explanation of what arguments the command does need. Click here to check your work, or for the answer if needed Expand source.