search

sterding / ea-utils

Automatically exported from code.google.com/p/ea-utils
0 stars 1 forks source link

fastq-multx when barcode is in header between # and / symbols? #30

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. I have fastq files where the barcode was written in the header row between 
symbols # (on the left) and / (on the right)
2. To complicate things further, we used 6-bases barcodes, and the machine was 
set to sequence 8-bases barcodes. We know for a fact that our barcode is the 
first 6 bases after the # symbol. The last two bases should always be "AT" in 
our case
3. I used the -B option with a file giving the 6-bases barcodes.

What is the expected output? What do you see instead?
I observed 88% "unmatched" reads (150.174.690 out of total 170.571.259). The 
log mentioned "End used: end", stating it used the 3' of the read. Is there a 
way to make it look into the header?

What version of the product are you using? On what operating system?
Working on Ubuntu Linux, ea-utils.1.1.2-537.tar.gz

Please provide any additional information below.

Original issue reported on code.google.com by kevinru...@gmail.com on 20 Mar 2014 at 12:42

GoogleCodeExporter commented 9 years ago 
Can you attach/upload a couple subsets of data (zcat file | head -100)... so I 
can see what you're talking about?   I can probably add support for "header 
embedded" codes pretty quickly... esp since this is a fairly common case.

Original comment by earone...@gmail.com on 2 May 2014 at 4:58

GoogleCodeExporter commented 9 years ago 
Here you go!

These are the top 25 paired reads extracted from raw data files.

Again, note that the real barcode is only the first 6 nucleotides after the # 
symbol, not the full 8 bases sequenced.

Thanks a lot for looking into that!
Kevin

Original comment by kevinru...@gmail.com on 2 May 2014 at 5:09

Attachments:

GoogleCodeExporter commented 9 years ago 
Issue 31 has been merged into this issue.

Original comment by earone...@gmail.com on 9 Jul 2014 at 2:28

GoogleCodeExporter commented 9 years ago 
finally done, release 762 or greater.

Original comment by earone...@gmail.com on 15 Aug 2014 at 3:05

GoogleCodeExporter commented 9 years ago

Original comment by earone...@gmail.com on 15 Aug 2014 at 3:05

GoogleCodeExporter commented 9 years ago 
Hi, I'm facing the same problem having the barcodes in the header row. What is 
not clear is how I can get and install the latest release (>762)? since the one 
I can download is release 686.
Thanks for help!

Maurizio

Original comment by maurizio...@gmail.com on 20 Aug 2014 at 10:06

GoogleCodeExporter commented 9 years ago 
You need to do the following:

https://code.google.com/p/ea-utils/source/checkout

NOTE: We're probably not going to stamp a new release until the test 
architecture is all worked out.

Original comment by earone...@gmail.com on 20 Aug 2014 at 5:08