Edwards Lab Tools

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Welcome to the Edwards Lab Q&A site. You can ask questions about any of the tools develop in our lab, which includes suggestions, issues, general questions. To find a list of tools we have developed, take a look at http://edwards.sdsu.edu/labsite/index.php/software
Tools include PRINSEQ, TagCleaner, DeconSeq, riboPicker, Xipe-Totec, RTMg, crAss, Scaffold_builder, PHACTS, Phage Proteomic Tree, Phage Eco-Locator, PhiSpy, Mobile Metagenomics, ...

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shapi...@gmail.com

1/12/20

ERROR: input file for -fastq is in UNKNOWN format not in FASTQ format

Hey there, I'm using PRINSEQ-lite 0.20.4 wrapped with pipeline used in my lab. It seems the

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ERROR: input file for -fastq is in UNKNOWN format not in FASTQ format

Hey there, I'm using PRINSEQ-lite 0.20.4 wrapped with pipeline used in my lab. It seems the

1/12/20

Letícia Cavalcante

5/17/18

Problems in clean paired end metagenomes

Hello, everyone, We're using PRINSEQ to make the quality control in some publicly available

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Problems in clean paired end metagenomes

Hello, everyone, We're using PRINSEQ to make the quality control in some publicly available

5/17/18

millipede...@gmail.com

5/10/18

Use of uninitialized value $qual in scalar chomp

When I run prinseq-lite with my fastq files (generated from fastq-dump for NCBI SRA data), I get the

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Use of uninitialized value $qual in scalar chomp

When I run prinseq-lite with my fastq files (generated from fastq-dump for NCBI SRA data), I get the

5/10/18

millipede...@gmail.com2

5/10/18

Prinseq standalone input erro

I actually re-did my fastq-dump and got fastq files that will work with prinseq...to some degree. I

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Prinseq standalone input erro

I actually re-did my fastq-dump and got fastq files that will work with prinseq...to some degree. I

5/10/18

Letícia Cavalcante

4/27/18

PRINSEQ Paired-end reads and outputs files

Hello, everyone, We're using PRINSEQ to make the quality control in some publicly available

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PRINSEQ Paired-end reads and outputs files

Hello, everyone, We're using PRINSEQ to make the quality control in some publicly available

4/27/18

met...@cbs.dtu.dk, helena....@gmail.com2

5/3/18

PRINSEQ - service temporary unavailable

I'm having the same problem, I can not use PRINSEQ in the browser. Please fix this.

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PRINSEQ - service temporary unavailable

I'm having the same problem, I can not use PRINSEQ in the browser. Please fix this.

5/3/18

ckhi...@gmail.com

1/4/18

Prinseq Tool usage

Hi, This is hithesh i'm looking the usage for gunzip paired end fastq files. Thanks in Advance

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Prinseq Tool usage

Hi, This is hithesh i'm looking the usage for gunzip paired end fastq files. Thanks in Advance

1/4/18

sh82...@gmail.com

2/27/17

Problem filtering fastq files with PRINSEQ

Hi there, I am using PRINSEQ for filtering my paired end illumina fastq files based on quality score,

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Problem filtering fastq files with PRINSEQ

Hi there, I am using PRINSEQ for filtering my paired end illumina fastq files based on quality score,

2/27/17

david.p...@gmail.com

2/1/17

Prinseq getting sleeping Status "D"

Hi, I have a lot of data to analyse but i have a problem. I've made a bash script to computize my

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Prinseq getting sleeping Status "D"

Hi, I have a lot of data to analyse but i have a problem. I've made a bash script to computize my

2/1/17

yurim...@gmail.com

1/27/17

Hi, I tried filtering and trimming using prinseq with the options below. -trim_tail_left 5 -

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Hi, I tried filtering and trimming using prinseq with the options below. -trim_tail_left 5 -

1/27/17

11/4/16

Output same number of sequences in singletons and paired files

Running prinseq-lite with both files of paired-end reads, I obtained the kind of result. All

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Output same number of sequences in singletons and paired files

Running prinseq-lite with both files of paired-end reads, I obtained the kind of result. All

11/4/16

10/14/16

Does prinseq-lite output complextity score?

Hi, I'm trying to figure out where prinseq-lite outputs the Entropy/Dust scores. I don't see

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Does prinseq-lite output complextity score?

Hi, I'm trying to figure out where prinseq-lite outputs the Entropy/Dust scores. I don't see

10/14/16

9/21/16

Prinseq-lite : generates single line with 160,000,000 characters

I am currently running prinseq-lite-0.20.4. The command I ran was perl prinseq-lite-0.20.4/prinseq-

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Prinseq-lite : generates single line with 160,000,000 characters

I am currently running prinseq-lite-0.20.4. The command I ran was perl prinseq-lite-0.20.4/prinseq-

9/21/16

9/8/16

-derep need very high memory

I use commands as below: gzip -dc /data/SRR606249_1.fastq.gz |perl prinseq-lite.pl -fastq stdin -

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-derep need very high memory

I use commands as below: gzip -dc /data/SRR606249_1.fastq.gz |perl prinseq-lite.pl -fastq stdin -

9/8/16

met...@cbs.dtu.dk, Kate2

9/1/16

Error message when uploading paired-end FASTQ files to PRINSEQ

I just ran two files through Prinseq as paired end. And it worked fine. They were named "one.

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Error message when uploading paired-end FASTQ files to PRINSEQ

I just ran two files through Prinseq as paired end. And it worked fine. They were named "one.

9/1/16

josefw...@yahoo.com

5/24/16

WebPrinseq not working

Hello, I would like to use Web PrinSeq to generate graph files. I have noticed that the sever has

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WebPrinseq not working

Hello, I would like to use Web PrinSeq to generate graph files. I have noticed that the sever has

5/24/16

frenett...@gmail.com

5/10/16

PRINSEQ Web-Based Version Not Found

Hi Edwards Lab, Sending a quick note to ask if the PRINSEQ web-based version is still available or if

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PRINSEQ Web-Based Version Not Found

Hi Edwards Lab, Sending a quick note to ask if the PRINSEQ web-based version is still available or if

5/10/16

mcss...@gmail.com

4/3/16

Duplicates similarity

What are exactly the similarity and coverage that Prinseq consider to establish two sequences as

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Duplicates similarity

What are exactly the similarity and coverage that Prinseq consider to establish two sequences as

4/3/16

david.p...@gmail.com

3/31/16

Hi, i would like to know which is the formula used to calculate the quality score mean in the option

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Hi, i would like to know which is the formula used to calculate the quality score mean in the option

3/31/16

ultr...@gmail.com

3/5/16

Graph for tag sequences

Hello, I ran prinseq with the output all graphs option (default) as seen below /opt/prinseq-lite-0.20

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Graph for tag sequences

Hello, I ran prinseq with the output all graphs option (default) as seen below /opt/prinseq-lite-0.20

3/5/16

zagos...@gmail.com, … dni...@uci.edu7

12/13/18

Error: File upload stopped by extension

Hi, I am having the same issue today. I am thankful for any help. Devan

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Error: File upload stopped by extension

Hi, I am having the same issue today. I am thankful for any help. Devan

12/13/18

ari...@gmail.com

10/2/15

unable to access dataset and upload files from today 01:00 GMT (Errors not sure what to do/File upload stopped by extension)

I have been using Prinseq in webmode for the past 2 days with the option to keep it for 1 week/168 h.

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unable to access dataset and upload files from today 01:00 GMT (Errors not sure what to do/File upload stopped by extension)

I have been using Prinseq in webmode for the past 2 days with the option to keep it for 1 week/168 h.

10/2/15

9/6/15

After running the prinseq I found no output. EMERGENCY!!!!!

Sir, I wanted to use prinseq to filter my fastq files. After running this command it seemed

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After running the prinseq I found no output. EMERGENCY!!!!!

Sir, I wanted to use prinseq to filter my fastq files. After running this command it seemed

9/6/15

8/30/15

Command line example for filtering fastq files according to quality score

Hi there, I wanted to filter my paired end fastq files according to their quality score. Can anyone

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Command line example for filtering fastq files according to quality score

Hi there, I wanted to filter my paired end fastq files according to their quality score. Can anyone

8/30/15

perrin...@gmail.com, Kate2

8/6/15

PRINSEQ Paired-end reads input format data

It looks as though they are not already marked. The .1 and .2 appear to be the sequence number. It

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PRINSEQ Paired-end reads input format data

It looks as though they are not already marked. The .1 and .2 appear to be the sequence number. It

8/6/15

data.bi...@gmail.com

6/29/15

How to use perl prinseq-lite in Windows 7 Strawberry Perl?

Hi, I tried this in linux and it is working well. my_home> prinseq-lite.pl -verbose -fasta

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How to use perl prinseq-lite in Windows 7 Strawberry Perl?

Hi, I tried this in linux and it is working well. my_home> prinseq-lite.pl -verbose -fasta

6/29/15

ana.usie...@gmail.com

3/3/15

Generate the report without preprocessing data with standalone version

Hi, before do anything with my data, I would like to have a report of the data as the web tool does.

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Generate the report without preprocessing data with standalone version

Hi, before do anything with my data, I would like to have a report of the data as the web tool does.

3/3/15

k.ma...@gmail.com

2/25/15

Making only stats with prinseq

Hello everyone, I have a question regarding the analysis done by prinseq. I made prinseq-lite

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Making only stats with prinseq

Hello everyone, I have a question regarding the analysis done by prinseq. I made prinseq-lite

2/25/15

fa...@cornell.edu

2/16/15

Error when trying to generate an HTML report

Hello, I received the following error when trying to generate an HTML report: An error occured when

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Error when trying to generate an HTML report

Hello, I received the following error when trying to generate an HTML report: An error occured when

2/16/15

Rob Edwards, megha...@gmail.com2

2/26/15

The Solution to Prinseq File Upload Stopped by Extension

DeconSeq's file upload has stopped. Please fix it.

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The Solution to Prinseq File Upload Stopped by Extension

DeconSeq's file upload has stopped. Please fix it.

2/26/15

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