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Manasa Ramakrishna
9/5/18
How to get fastq-multx to recognize barcodes that are not at the start of the read
Dear Erik, Thank you so much for writing fastq-multx as it is fantastic and quick for de-multiplexing
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How to get fastq-multx to recognize barcodes that are not at the start of the read
Dear Erik, Thank you so much for writing fastq-multx as it is fantastic and quick for de-multiplexing
9/5/18
Raquel Xavier
,
Ruby setiawan
2
11/30/17
error in make command in MAC
I also have a same problem installing ea-utils on MacOS, this is what I got: ````````````````````````
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error in make command in MAC
I also have a same problem installing ea-utils on MacOS, this is what I got: ````````````````````````
11/30/17
Pete Light
11/29/16
HELP! :( Exception when running EA utils :(
Hey guys, bit of a EAUtils newbie here but from what I can gather I simply had to install, select the
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HELP! :( Exception when running EA utils :(
Hey guys, bit of a EAUtils newbie here but from what I can gather I simply had to install, select the
11/29/16
n.bha...@celmatix.com
2/28/16
fastq_multx help
Hi, I am running fastq_multx to demultiplex Illumina files. I have 2 paired-end files:
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fastq_multx help
Hi, I am running fastq_multx to demultiplex Illumina files. I have 2 paired-end files:
2/28/16
Alexander Jueterbock
10/19/15
quality filtering
Hello, I would like to ask how the removal of base pairs below a quality threshold is done. Are all
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quality filtering
Hello, I would like to ask how the removal of base pairs below a quality threshold is done. Are all
10/19/15
Kimberly Robasky
10/14/15
New github repo for ea-utils!
All, Now that the google code ea-utils repo is read-only, the company formerly known as "
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New github repo for ea-utils!
All, Now that the google code ea-utils repo is read-only, the company formerly known as "
10/14/15
liisa...@hotmail.com
9/8/15
fastq-multx not returning correct number of fastq files
Hi, I am using fastq-multx with the -l flag in a bash script fastq-multx -l $1 $2 $3 -o %.R2.fastq -o
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fastq-multx not returning correct number of fastq files
Hi, I am using fastq-multx with the -l flag in a bash script fastq-multx -l $1 $2 $3 -o %.R2.fastq -o
9/8/15
Yiping Zhan
9/8/15
behavior of fastq-mcf for two adaptor clipping toy examples
Hello Erik and experienced EA Utils users, I'm puzzled by the behavior of fastq-mcf in the
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behavior of fastq-mcf for two adaptor clipping toy examples
Hello Erik and experienced EA Utils users, I'm puzzled by the behavior of fastq-mcf in the
9/8/15
Sanjeev Sariya
,
Yiping Zhan
5
9/2/15
which version of ea-utils | fastq-join?
Hello Zhan, Thanks for helping in this naive problem. -----------------------------------------------
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which version of ea-utils | fastq-join?
Hello Zhan, Thanks for helping in this naive problem. -----------------------------------------------
9/2/15
Sanjeev Sariya
9/2/15
stitch reads with percent mismatch
Hi ea-utils team, I'm using fastq-join to stitch 16S reads: V3-V4 region, length ~460 bp.
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stitch reads with percent mismatch
Hi ea-utils team, I'm using fastq-join to stitch 16S reads: V3-V4 region, length ~460 bp.
9/2/15
Sanjeev Sariya
,
Jason Powers
3
8/4/15
paper for ea-utils?
Hello Jason, Thanks for your reply. Cheers, Sanjeev -------------------------------------------------
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paper for ea-utils?
Hello Jason, Thanks for your reply. Cheers, Sanjeev -------------------------------------------------
8/4/15
Luisa B.
,
Erik Aronesty
4
8/1/15
fastq-multx - Skipped because of distance < 2?
Yes that is 100% correct. On Wed, Jul 29, 2015 at 8:33 AM, Luisa B. <luisa.b...@gmail.com>
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fastq-multx - Skipped because of distance < 2?
Yes that is 100% correct. On Wed, Jul 29, 2015 at 8:33 AM, Luisa B. <luisa.b...@gmail.com>
8/1/15
Wimalanathan Kokulapalan
,
Erik Aronesty
2
7/6/15
What is the quality format used in fastq-multx? Is is Sanger or Solexa?
Both. On Thursday, April 9, 2015 at 10:09:24 AM UTC-4, Wimalanathan Kokulapalan wrote: When using
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What is the quality format used in fastq-multx? Is is Sanger or Solexa?
Both. On Thursday, April 9, 2015 at 10:09:24 AM UTC-4, Wimalanathan Kokulapalan wrote: When using
7/6/15
Gang Chen
,
Erik Aronesty
3
7/6/15
fastq-mcf's window option for quality trimming
This is correct, it's a sliding average window. This prevents a single good quality base from
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fastq-mcf's window option for quality trimming
This is correct, it's a sliding average window. This prevents a single good quality base from
7/6/15
Tejaswi Yarra
,
Jason Powers
3
6/5/15
Using -D option
Thank you very much for the explanation Jason! Very sorry for the late reply, I did not check back
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Using -D option
Thank you very much for the explanation Jason! Very sorry for the late reply, I did not check back
6/5/15
richard rodrigues
2
5/23/15
MiSeq seq of samples prepared using Illumina's Nextera protocol
I think (ii) should be reverse complement of rev overhang_adapter-rev_primer from end of read 1 On
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MiSeq seq of samples prepared using Illumina's Nextera protocol
I think (ii) should be reverse complement of rev overhang_adapter-rev_primer from end of read 1 On
5/23/15
Sam White
,
Erik Aronesty
2
4/8/15
Problem compiling on OSX 10.7.5
you can either 1. install the gnu scientific library or 2. make the tools ou need only (make fast-mcf
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Problem compiling on OSX 10.7.5
you can either 1. install the gnu scientific library or 2. make the tools ou need only (make fast-mcf
4/8/15
lanc...@genomics.com.tw
, …
Erik Aronesty
4
4/8/15
fastq-multx for dualbarcode-indexed library
we have done demux withe dual-barcoded paired end data a lot, just never embedded in the files. you
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fastq-multx for dualbarcode-indexed library
we have done demux withe dual-barcoded paired end data a lot, just never embedded in the files. you
4/8/15
Eric P
,
Erik Aronesty
2
4/8/15
installing ea utils on Linux mint
- the warnings are mostly fine... sizets should be unsigned thats all. - unless you're using
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installing ea utils on Linux mint
- the warnings are mostly fine... sizets should be unsigned thats all. - unless you're using
4/8/15
Eugenia Golovina
, …
Erik Aronesty
8
4/8/15
Fastq-mcf behavior on different operating systems
thats a pretty old version, you might want to build from source, or download from here: https://drive
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Fastq-mcf behavior on different operating systems
thats a pretty old version, you might want to build from source, or download from here: https://drive
4/8/15
adam...@berkeley.edu
,
Erik Aronesty
2
2/24/15
ea-utils build problem on Centos 5
try ruynning autoconf/automake in the sparsehash folder? On Friday, October 24, 2014 at 6:42:42 PM
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ea-utils build problem on Centos 5
try ruynning autoconf/automake in the sparsehash folder? On Friday, October 24, 2014 at 6:42:42 PM
2/24/15
Kendell Clement
,
Erik Aronesty
2
2/24/15
Wildcards in Adapters
N's or even X's do work as wildcards, yes. They count as "always mismatch". Then
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Wildcards in Adapters
N's or even X's do work as wildcards, yes. They count as "always mismatch". Then
2/24/15
Rob van Nues
,
Erik Aronesty
3
2/24/15
compilation on slackware64 14.1
- tidx isn't necessary for most ofd what people do with ea-utils that's a utility for
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compilation on slackware64 14.1
- tidx isn't necessary for most ofd what people do with ea-utils that's a utility for
2/24/15
daie...@yahoo.com
,
Erik Aronesty
2
2/24/15
fastq-mcf for removing target specific primer sequences
I would not use fastq-mcf to trim primer sequences. Primers will be present in their entirety,
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fastq-mcf for removing target specific primer sequences
I would not use fastq-mcf to trim primer sequences. Primers will be present in their entirety,
2/24/15
Eckart Stolle
,
Erik Aronesty
2
2/24/15
fastq-multx support of custom dual-barcodes with variable length
Should work fine. I have learned that mcf will not trim the second barcode off of the sequence read,
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fastq-multx support of custom dual-barcodes with variable length
Should work fine. I have learned that mcf will not trim the second barcode off of the sequence read,
2/24/15
Mike R
, …
Erik Aronesty
10
2/24/15
Problem with compiling ea-utils on Mac OS 10.9
I think this solution is the best: make sparsehash make Probablly the makefile is not correct for MAC
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Problem with compiling ea-utils on Mac OS 10.9
I think this solution is the best: make sparsehash make Probablly the makefile is not correct for MAC
2/24/15
Erin
1/9/15
number of joined reads
Hello, I used fastq to join forward and reverse reads from Illumina, below: # Join forward and
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number of joined reads
Hello, I used fastq to join forward and reverse reads from Illumina, below: # Join forward and
1/9/15
Cynthia Gibas
, …
Colleen Kellogg
15
12/3/14
ea-utils on Mavericks (10.9.3)
Hello, I have been trying to compile this on a Mavericks machine as well, with no success. Did anyone
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ea-utils on Mavericks (10.9.3)
Hello, I have been trying to compile this on a Mavericks machine as well, with no success. Did anyone
12/3/14
Brittany Demmitt
, …
brittany
9
9/18/14
fastq-mcf barcode file
I see, thanks! :) Britt On Thursday, September 18, 2014 9:20:18 AM UTC-6, Erik Aronesty wrote: Sorry,
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fastq-mcf barcode file
I see, thanks! :) Britt On Thursday, September 18, 2014 9:20:18 AM UTC-6, Erik Aronesty wrote: Sorry,
9/18/14
Brittany Demmitt
, …
brittany
12
9/18/14
fastq-join quality score mismatch base
Ahhh I see, that makes sense. Thank you so much!!!! :-) Britt On Thursday, September 18, 2014 8:49:36
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fastq-join quality score mismatch base
Ahhh I see, that makes sense. Thank you so much!!!! :-) Britt On Thursday, September 18, 2014 8:49:36
9/18/14