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Hello,
I am searching large (~25gb) DNA sequence data in fasta short read format:

>ReadName
ACGTACGTACGT...[150charactersPerRead]

for short tandem repeats, meaning instances of any 2-6...

I have a tab-delimited file containing a large genetic dataset with binary base calls, in this format:

Chr7 26021407 1/1:0,0,0:5 1/1:0,0,0:5 1/1:0,0,0:5
Chr7 26022023 1/1:0,0,0:3 1/1:0,0,0:3...

Hello,
I am working with next-gen short-read sequence data, which we receive in 3 fastq files. These are arranged in 4-line groups for each read:
line1: read identifier, beginning, e.g.,...

Thanks Jim, I just figured this out as well (still quite new to this!)

Hello,
I've searched this forum and others for a solution to my problem but nothing seems just right, I'm hoping I can get some help (seems like this should be easy, and I apologize if I've missed...

You're right, this is just a short snippet taken from the dataset so I didn't follow that rule in the example. If just one sample of the 41 differs, it's not informative, but it's not the end of the...

Alright, it works ok on the example, but when it gets more complicated it starts to not handle the missing characters in the same way, and ultimately breaks down completely with a few full-length...

Thanks for the reply, I tried that code and it duplicated every site on each line, so the output is 56024 sites (I was off by 2 before when I wrote 28014).

Hello,
I have a nexus alignment file that looks like this:


bar101_min2covg_binarynex 11001-100111
bar102_min2covg_binarynex 110010010011
bar103_min2covg_binarynex 11101010--11
etc.

There...

Perfect, thanks!

Hi,
I have searched the forums for a solution but I haven't found a perfect answer, and I'm a bit of a novice, so I hope someone can help:

I have 2 files:

file1:

Chr1 139311 1/1:37,3,0:19...