[cement_head]

You can try Mason. Maybe that is what you need.

Thanks for the URL to the software and the paper.

[howen]

You can try Mason. Maybe that is what you need.

[abolia]

Yup, got you..

Thanks for the help.

Ashini.

[Brian Bushnell]

The coverage distribution would look like Colorado/New Mexico, flat with plateaus:



But without the scree slopes at the bottom.

[abolia]

Hi Brian,

One more last question, I have this idea and just want to confirm this with someone knowledgeable.

How about if I use getfasta to extract regions (given in the BED file) from my rearranged fasta file (lets call fasta file 1) and then use randomreads.sh to generate reads on that chopped fasta file (lets call fasta file 2, i.e. output of getfasta).
In next step, simulatenously generate more random reads from the original fasta file 1.
Now merge the two fastq files that you get from these 2 steps. So basically we are throwing some additional reads so that distribution can become more gaussian like rather than flat one.

Does this make sense? Do you think it might work or am I missing something here.

Thanks again,
Ashini.

[abolia]

Thanks Brian,
Yeah I don't think there is anything like that either. I will give it a try and try to do it myself.

Thanks for your reply.
Ashini.

[Brian Bushnell]

The distribution would be relatively flat. I don't have any tools that can simulate read generation from baited regions, and I don't know of any. It sounds like something you would have to write yourself. But, RandomReads generates reads annotated by their genomic origin, so it's possible to generate a flat distribution with it, then postprocess them and randomly discard reads with a probability based on the distance from the center of the nearest bait to achieve your goal. It would take a bit of work, of course.

[abolia]

Thanks GenoMax, your answers looks good. But won't this generate a very uniform distribution around the regions specified in the BED file. I want to have more of gaussian kinda distribution for my reads. Any thoughts if it can do this?

Thanks,
Ashini.

[GenoMax]

Hi all,
I want to generate reads for one of my rearranged genomes using a list of genomic coordinates in a BED file. The whole idea is to generate random DNA fragments from designated target regions.

I tried using Wessim simulator, but it throws me bunch of errors and when I tried contacting their team, they said they no longer work on that project.

Does anyone has any idea how to do this? Any help would be really great.

Thanks,
Ashini.

If I understand this right ...

You could use getfasta from BedTools (http://bedtools.readthedocs.org/en/l.../getfasta.html) to extract regions that you are interested in as fasta. Then use @Brian's randomreads.sh program.

[abolia]

Hi all,
I want to generate reads for one of my rearranged genomes using a list of genomic coordinates in a BED file. The whole idea is to generate random DNA fragments from designated target regions.

I tried using Wessim simulator, but it throws me bunch of errors and when I tried contacting their team, they said they no longer work on that project.

Does anyone has any idea how to do this? Any help would be really great.

Thanks,
Ashini.

[cement_head]

Ok, thanks!

[Brian Bushnell]

This depends on exactly what you want to do with transcripts shorter than 250bp, but... there are 2 ways to do this:

randomreads.sh ref=transcriptome.fa out=synth.fq.gz reads=100000 len=100 paired interleaved mininsert=250 maxinsert=250

Or, if you shred it some way so you already have 250bp single-ended reads:

bbfakereads.sh in=shreds.fq out=pairs.fq length=100

I wrote that specifically for this purpose Incidentally, both of these commands will produce interleaved reads; you can convert between interleaved and dual-file paired, or between fasta and fastq, with reformat.sh, if you have things in the wrong format.

The first command will only produce inserts of exactly 250bp, and the second will only produce inserts of exactly the length of the input sequences.

[cement_head]

(Hopefully) last question(s):

I'd like to take a transcriptome (in the form of a file that contains all the FASTAs) - actually the ZF transcriptome and in silico fragment it into 250 bp "insert" sizes. Then I'd like to generate a pair of 100 bp PE reads from each fragment.

In other words, if I have 100,000 fragments of 250 bp, I'd like to end up with 200,000 PE reads - one set corresponding to each of the 100,000 fragments. I know this is artificial, but because we're trying to check code, we'd like to be very defined and controlled in this first test.

Thanks,
Andor

[Brian Bushnell]

Incidentally, there's another tool that will do that too, Shred:

shred.sh in=ref.fasta out=reads.fastq length=200

The difference is that RandomReads will make reads in a random order from random locations, ensuring flat coverage on average, but it won't ensure 100% coverage unless you generate many fold depth. Shred, on the other hand, gives you exactly 1x depth and exactly 100% coverage (and is not capable of modelling errors). So, the use-cases are different.

[cement_head]

Yes, it will. Any fasta is acceptable. You can't do anything regarding custom differential expression, though; it tries to generate a flat distribution.

Great! That's perfect - I need to "shred" a transcriptome so that I can use it to test a tool I'm making for molecular indexing. Thanks