AftrRAD

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Welcome to the AftrRAD google group! AftrRAD is a bioinformatic pipeline for assembling and genotyping restriction site-associated DNA sequence (RADseq) data. Feel free to use this forum to ask questions, make comments, report bugs, or have general discussions related to AftrRAD. Many updates will be announced/posted here first, so if you're using the program, we encourage you to join the group and either check back often, or sign up for e-mail notifications.

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Stefanie Farrington, Mike Sovic10

1/3/18

AftrRAD.pl output getting stuck

Hi Stefanie, Sorry you're having these problems, know this is frustrating, but I'm cautiously

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AftrRAD.pl output getting stuck

Hi Stefanie, Sorry you're having these problems, know this is frustrating, but I'm cautiously

1/3/18

xiaolon...@gmail.com, Mike Sovic2

6/27/16

The running time of searching unique sequence for potentially allelic read pairs

Hi, This is probably normal. The good news is that this step will speed up somewhat as it runs -

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The running time of searching unique sequence for potentially allelic read pairs

Hi, This is probably normal. The good news is that this step will speed up somewhat as it runs -

6/27/16

JB, Mike Sovic3

3/29/16

Problem with output files

Thanks, Mike. I did rerun it changing to pctScored argument to 80 and this helped. I have minReads

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Problem with output files

Thanks, Mike. I did rerun it changing to pctScored argument to 80 and this helped. I have minReads

3/29/16

Tatiana Barroca, Mike Sovic2

3/11/16

Question about reads sizes

Hello Tatiana, You are correct that you should not include reads of different lengths in AftrRAD (at

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Question about reads sizes

Hello Tatiana, You are correct that you should not include reads of different lengths in AftrRAD (at

3/11/16

JB, Mike Sovic5

3/4/16

Question about quality scores

Hi Mike, Thanks for all of the advice and time you put into answering my question. I'm toying

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Question about quality scores

Hi Mike, Thanks for all of the advice and time you put into answering my question. I'm toying

3/4/16

leanne....@gmail.com, … Mike Sovic12

2/19/16

Running Demultiplexed Data

Hi Leanne, Well, my first thought is that there are sequences of different lengths in the dataset.

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Running Demultiplexed Data

Hi Leanne, Well, my first thought is that there are sequences of different lengths in the dataset.

2/19/16

2/16/16

AftrRAD Version 5.0

Hi All, Attached to this message is AftrRAD version 5.0 (also now available on the GitHub site and my

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AftrRAD Version 5.0

Hi All, Attached to this message is AftrRAD version 5.0 (also now available on the GitHub site and my

2/16/16

jmwhi...@mix.wvu.edu, Mike Sovic2

2/11/16

R error message

Yep - I expect you're right that the problem is associated with one of the output files from the

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R error message

Yep - I expect you're right that the problem is associated with one of the output files from the

2/11/16

quy...@gmail.com, Mike Sovic4

2/8/16

No such file or directory at AftrRAD.pl line 513

Hi Quynh, No, I don't think you should get the "killed" message. Never seen it before,

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No such file or directory at AftrRAD.pl line 513

Hi Quynh, No, I don't think you should get the "killed" message. Never seen it before,

2/8/16

yexiay...@gmail.com, Mike Sovic2

12/18/15

How much memory do I need when deal with large data?

Hi, I don't think the sequence length should matter - as long as all sequences are the same

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How much memory do I need when deal with large data?

Hi, I don't think the sequence length should matter - as long as all sequences are the same

12/18/15

Pedro Andrade, Mike Sovic14

10/27/15

Genotype_Edit.R

Hmm…Having the SortedIndividualX.txt files, but not having the UniqueWithCountsIndividualX.txt is

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Genotype_Edit.R

Hmm…Having the SortedIndividualX.txt files, but not having the UniqueWithCountsIndividualX.txt is

10/27/15

Mike Sovic, Bartosz Ulaszewski3

10/17/15

Updated AftrRAD Parallel Version Draft with Bug Fix Related To Demultiplexed Data

Hi Bartosz, Thanks very much for the feedback! I don't think we've ever tried running the

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Updated AftrRAD Parallel Version Draft with Bug Fix Related To Demultiplexed Data

Hi Bartosz, Thanks very much for the feedback! I don't think we've ever tried running the

10/17/15

tngth...@gmail.com, Mike Sovic2

10/17/15

Runnng Demultiplexed Data Files

Hi Thomas, 1.) You were right in removing the 'DataPath' argument - the default should be

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Runnng Demultiplexed Data Files

Hi Thomas, 1.) You were right in removing the 'DataPath' argument - the default should be

10/17/15

Bartosz Ulaszewski, Mike Sovic3

10/15/15

Simple question pvalHigh

Hi Mike, Thanks for the answer, I'll try to check my data as you suggested, maybe something will

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Simple question pvalHigh

Hi Mike, Thanks for the answer, I'll try to check my data as you suggested, maybe something will

10/15/15

jose luis acosta, Mike Sovic10

9/25/15

Barcodes with different length size.

Hi Jose, This AllReadsAndDepths file contains every unique sequence read in the dataset, and the

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Barcodes with different length size.

Hi Jose, This AllReadsAndDepths file contains every unique sequence read in the dataset, and the

9/25/15

Mike Sovic, Bartosz Ulaszewski7

6/10/15

AftrRAD Parallel Version Draft

OK, I think I see what's causing the errors (or at least some of them). Two things… 1.) It looks

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AftrRAD Parallel Version Draft

OK, I think I see what's causing the errors (or at least some of them). Two things… 1.) It looks

6/10/15

Ninh Vu, Mike Sovic3

5/12/15

Parallel_Draft stop abruptly

Hi Ninh, Is it possible you don't have enough free disk space for the run? See my posts under the

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Parallel_Draft stop abruptly

Hi Ninh, Is it possible you don't have enough free disk space for the run? See my posts under the

5/12/15

ninh...@gmail.com, Mike Sovic4

5/8/15

missing TemGenotypes.txt file after AftrRAD.pl run

Great - thanks for letting us know, Ninh. Mike

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missing TemGenotypes.txt file after AftrRAD.pl run

Great - thanks for letting us know, Ninh. Mike

5/8/15

Thierry Gosselin, Mike Sovic2

5/7/15

Problem running the script

Hi Tierry, No, there's a problem there. It looks to me like it doesn't know where to find the

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Problem running the script

Hi Tierry, No, there's a problem there. It looks to me like it doesn't know where to find the

5/7/15

parisjo...@googlemail.com, Mike Sovic12

5/6/15

Perl errors in AftrRAD.pl

Hi Josie, Thanks very much for the update. This sort of feedback is very helpful moving forward. This

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Perl errors in AftrRAD.pl

Hi Josie, Thanks very much for the update. This sort of feedback is very helpful moving forward. This

5/6/15

seeholz...@gmail.com, Mike Sovic2

4/30/15

mafft on remote cluster

Hi Glenn, I'm not really sure about this. I see some instructions for installation without root

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mafft on remote cluster

Hi Glenn, I'm not really sure about this. I see some instructions for installation without root

4/30/15

Thierry Gosselin, Mike Sovic2

3/25/15

Hi Thierry, My first guess is that you need to unzip your data file. With a .gz file, you should be

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Hi Thierry, My first guess is that you need to unzip your data file. With a .gz file, you should be

3/25/15

3/24/15

OutputFastSimCoal Bugs

OK, attached to this message is an updated version of the script to output joint site frequency

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OutputFastSimCoal Bugs

OK, attached to this message is an updated version of the script to output joint site frequency

3/24/15

3/4/15

ScoreDuplicates.pl Bug and Work-Around

Hi All, It looks like ScoreDuplicates.pl in version 4.1 has a bug that causes the script to crash

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ScoreDuplicates.pl Bug and Work-Around

Hi All, It looks like ScoreDuplicates.pl in version 4.1 has a bug that causes the script to crash

3/4/15

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