Trans-ABySS

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o k, Ka Ming Nip5

Sep 7

Error with reading input files

Thank you for suggestion, Ka Ming. I cannot install transabyss with conda because my computer does

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Error with reading input files

Thank you for suggestion, Ka Ming. I cannot install transabyss with conda because my computer does

Sep 7

Frederico Moraes Ferreira, Ka Ming Nip3

Jul 21

3 prime end enlongation

Hi Ming, Tanks for helping. I'm gonna give RNA-Bloom. I'll let to know the results. Best Fred

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3 prime end enlongation

Hi Ming, Tanks for helping. I'm gonna give RNA-Bloom. I'll let to know the results. Best Fred

Jul 21

Brian Mailloux, Ka Ming Nip3

6/15/20

Fwd: installing with higher kmer

Ka Ming, Thank you. I was copying a paper where they are assembling ribosomal RNA and used kmer from

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Fwd: installing with higher kmer

Ka Ming, Thank you. I was copying a paper where they are assembling ribosomal RNA and used kmer from

6/15/20

Charles Foster, Ka Ming Nip7

11/12/19

Assembly of multiple biological replicates/libraries

Hi Charles, There are benefits in removing low coverage sequencing errors early in the assembly

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Assembly of multiple biological replicates/libraries

Hi Charles, There are benefits in removing low coverage sequencing errors early in the assembly

11/12/19

Feng Tao, Ka Ming Nip4

10/7/19

You can name the read files anyway you want as long as the constituent read names matches for each

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You can name the read files anyway you want as long as the constituent read names matches for each

10/7/19

Yuri Vic, Ka Ming Nip2

2/25/19

[BUG] Build doesn't use multiple CPUs, making it much slower

Hi, Can you please create a GitHub issue if you have problem compiling ABySS? https://github.com/

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[BUG] Build doesn't use multiple CPUs, making it much slower

Hi, Can you please create a GitHub issue if you have problem compiling ABySS? https://github.com/

2/25/19

2/24/19

[BUG] configure fails to find std::hash when the clang compiler is used

| int | main () | { | if (sizeof ((std::hash<int>))) | return 0; | ; | return 0; | } configure:

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[BUG] configure fails to find std::hash when the clang compiler is used

| int | main () | { | if (sizeof ((std::hash<int>))) | return 0; | ; | return 0; | } configure:

2/24/19

Dr. M.D. Sharma, Ka Ming Nip2

9/24/18

Hi, The only components that uses the tmp directory is the ABySS modules and probably unix sort. So,

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Hi, The only components that uses the tmp directory is the ABySS modules and probably unix sort. So,

9/24/18

Ryan, Ka Ming Nip4

9/13/18

Hi Ryan, I don't think you misunderstood anything here. :) Do you have the genomic sequencing

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Hi Ryan, I don't think you misunderstood anything here. :) Do you have the genomic sequencing

9/13/18

Luciano C. Maia, … николай шмаков6

5/30/18

WHAT OUTPUT FILE I NEED USE?

I see, thank you very much понедельник, 28 мая 2018 г., 13:51:10 UTC+7 пользователь Ka Ming Nip

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WHAT OUTPUT FILE I NEED USE?

I see, thank you very much понедельник, 28 мая 2018 г., 13:51:10 UTC+7 пользователь Ka Ming Nip

5/30/18

Benedikt Athmer, Ka Ming Nip2

5/3/18

in silico read normalization

You may use that or you could just run diginorm from the khmer package: http://khmer-protocols.

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in silico read normalization

You may use that or you could just run diginorm from the khmer package: http://khmer-protocols.

5/3/18

Emily Stander, Ka Ming Nip5

3/14/18

ERROR: CMD ended with status code 2 and no *contigs.fa output

I will check this. Thank you so much for your help :) Kind regards, Emily Regards, Emily Stander (M.

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ERROR: CMD ended with status code 2 and no *contigs.fa output

I will check this. Thank you so much for your help :) Kind regards, Emily Regards, Emily Stander (M.

3/14/18

Brian Lawney, Ka Ming Nip2

2/8/18

Assembly with and without stranded option

Hi, When the strand-specific option is used, it is expected that the /2 reads are in the sense

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Assembly with and without stranded option

Hi, When the strand-specific option is used, it is expected that the /2 reads are in the sense

2/8/18

clin...@umn.edu, Ka Ming Nip2

1/2/18

In stall transabyss error: ImportError: site-packages/igraph/_igraph.so: undefined symbol: PyUnicodeUCS2_AsEncodedString

Hi, Sorry for the late reply. I am on vacation. It looks like there is a problem with importing the

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In stall transabyss error: ImportError: site-packages/igraph/_igraph.so: undefined symbol: PyUnicodeUCS2_AsEncodedString

Hi, Sorry for the late reply. I am on vacation. It looks like there is a problem with importing the

1/2/18

9/19/17

Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea

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Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea

9/19/17

Chrissie Madden, Ka Ming Nip5

7/24/17

Paired-end data - how to run it?

Hi Chrissie, The newer format should be supported. Can you report the exact error message? Also, were

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Paired-end data - how to run it?

Hi Chrissie, The newer format should be supported. Can you report the exact error message? Also, were

7/24/17

Dapeng Wang, Ka Ming Nip4

5/2/17

The strandness of Trans-ABySS

Hi Tom, You should blat a few of your reads to confirm that '.2' reads are sense to the

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The strandness of Trans-ABySS

Hi Tom, You should blat a few of your reads to confirm that '.2' reads are sense to the

5/2/17

Vinay Mittal, … Ka Ming Nip5

3/24/17

mpi error abyss-pe

Thanks Ka Ming. This is really helpful. Interestingly our servers got updated a while ago and they

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mpi error abyss-pe

Thanks Ka Ming. This is really helpful. Interestingly our servers got updated a while ago and they

3/24/17

dario.ka...@googlemail.com, Ka Ming Nip5

3/21/17

How to set seed length

Thank you very much for your help! :) Am Freitag, 17. März 2017 00:36:27 UTC+1 schrieb Ka Ming Nip:

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How to set seed length

Thank you very much for your help! :) Am Freitag, 17. März 2017 00:36:27 UTC+1 schrieb Ka Ming Nip:

3/21/17

bilal....@cemb.edu.pk, … Ka Ming Nip12

3/2/17

denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

Ok, then that is fine. Those are temporary files from ABySS, which is why you don't see them in

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denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

Ok, then that is fine. Those are temporary files from ABySS, which is why you don't see them in

3/2/17

tianhe yu, … Ben Vandervalk7

2/23/17

Benchmark for Abyss

Dear Ben, Thanks for your reply! That is what I am doing currently to profile abyss-pe. I will focus

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Benchmark for Abyss

Dear Ben, Thanks for your reply! That is what I am doing currently to profile abyss-pe. I will focus

2/23/17

2/21/17

Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

US Congressional Hearing of Saudi billionaire" maan Al Sanea " and Money Laundering with

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Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

US Congressional Hearing of Saudi billionaire" maan Al Sanea " and Money Laundering with

2/21/17

etarisal, Ka Ming Nip4

2/1/17

abyss-pe:370: recipe for target 'XX.fa' failed on de novo assembly

Hi Etarisal, 1. If you haven't done so already, you should consider removing lower quality bases

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abyss-pe:370: recipe for target 'XX.fa' failed on de novo assembly

Hi Etarisal, 1. If you haven't done so already, you should consider removing lower quality bases

2/1/17

BlrGenomics, Ka Ming Nip4

1/23/17

Error: usr/bin/abyss-pe:473: recipe for target 'transabyss-1.fa' failed

Hi, I did not see any error messages at all in the log you provided. Did Trans-ABySS work for our

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Error: usr/bin/abyss-pe:473: recipe for target 'transabyss-1.fa' failed

Hi, I did not see any error messages at all in the log you provided. Did Trans-ABySS work for our

1/23/17

Cameron Prybol, Ka Ming Nip4

7/2/16

error: No network interfaces were found for out-of-band communications. We require at least one available network for out-of-band messaging.

Hi Cameron, This is indeed an issue with your ABySS installation. Best to get help from abyss-users@

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error: No network interfaces were found for out-of-band communications. We require at least one available network for out-of-band messaging.

Hi Cameron, This is indeed an issue with your ABySS installation. Best to get help from abyss-users@

7/2/16

Brian Novogradac, Ka Ming Nip5

6/9/16

Recompile transabyss question

Thanks!!! On Tuesday, June 7, 2016 at 10:00:34 AM UTC-4, Brian Novogradac wrote: I need to recompile

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Recompile transabyss question

Thanks!!! On Tuesday, June 7, 2016 at 10:00:34 AM UTC-4, Brian Novogradac wrote: I need to recompile

6/9/16

John Cornelius, Ka Ming Nip2

6/6/16

Resuming transcriptome assembly

Hi John, If you are using version 1.5.*, then re-runing the same command would resume the assembly

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Resuming transcriptome assembly

Hi John, If you are using version 1.5.*, then re-runing the same command would resume the assembly

6/6/16

Brian Novogradac, Ka Ming Nip9

6/6/16

having problems with Trans-ABySS 1.5.3/python version

I got it to finally work by installing python igraph separately. Thank s again for your help !!! On

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having problems with Trans-ABySS 1.5.3/python version

I got it to finally work by installing python igraph separately. Thank s again for your help !!! On

6/6/16

sri lakshmy, … jean-philippe buffet22

5/12/16

Transabyss-error in running

Thanks a lot Ka Ming for your fast and clear answer ! I am trying to reconfigure abyss with this

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Transabyss-error in running

Thanks a lot Ka Ming for your fast and clear answer ! I am trying to reconfigure abyss with this

5/12/16

Yogeshwar Dhar, Ka Ming Nip7

5/4/16

Trans-Abyss output error

Thank u sir :) On Tue, May 3, 2016 at 9:50 PM, Ka Ming Nip <km...@bcgsc.ca> wrote: Trans-ABySS

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Trans-Abyss output error

Thank u sir :) On Tue, May 3, 2016 at 9:50 PM, Ka Ming Nip <km...@bcgsc.ca> wrote: Trans-ABySS

5/4/16

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