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add nosZ and qNOR #1

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jiarong
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@jiarong jiarong commented Feb 15, 2015

As title, "nosZ" in fungene pipe are divided into two.

HMM in originaldata directory are made by hmmer-3.1. I can not find hmmer-3.1_xander_patch in /mnt/research/rdp, so did not run prepare_gene_ref.sh

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Can you give more information about how you generate norB and qNOR
reference set? Thanks.

On Sun, Feb 15, 2015 at 1:44 AM, jiarong [email protected] wrote:

As title, "nosZ" in fungene pipe are divided into two.

HMM in originaldata directory are made by hmmer-3.1. I can not find
hmmer-3.1_xander_patch in /mnt/research/rdp, so did not run

prepare_gene_ref.sh

You can view, comment on, or merge this pull request online at:

#1
Commit Summary

  • add norB and qNOR
  • remove dash(-) in variable

File Changes

Patch Links:

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#1.

Qiong

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Do you have the alignment file to make norB hmm? I need to use HMMER 3.0 to
make the alignment because the patch is based on HMMER 3.0.

On Sun, Feb 15, 2015 at 1:44 AM, jiarong [email protected] wrote:

As title, "nosZ" in fungene pipe are divided into two.

HMM in originaldata directory are made by hmmer-3.1. I can not find
hmmer-3.1_xander_patch in /mnt/research/rdp, so did not run

prepare_gene_ref.sh

You can view, comment on, or merge this pull request online at:

#1
Commit Summary

  • add norB and qNOR
  • remove dash(-) in variable

File Changes

Patch Links:

—
Reply to this email directly or view it on GitHub
#1.

Qiong

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jiarong commented Feb 17, 2015

/mnt/research/tg/g/for_qiong/pick_group/norB.fasta

/mnt/research/tg/g/for_qiong/pick_group/qNOR.fasta

On Feb 17, 2015, at 3:47 PM, Qiong Wang [email protected] wrote:

Do you have the alignment file to make norB hmm? I need to use HMMER 3.0 to
make the alignment because the patch is based on HMMER 3.0.

On Sun, Feb 15, 2015 at 1:44 AM, jiarong [email protected] wrote:

As title, "nosZ" in fungene pipe are divided into two.

HMM in originaldata directory are made by hmmer-3.1. I can not find
hmmer-3.1_xander_patch in /mnt/research/rdp, so did not run

prepare_gene_ref.sh

You can view, comment on, or merge this pull request online at:

#1
Commit Summary

  • add norB and qNOR
  • remove dash(-) in variable

File Changes

Patch Links:

�
Reply to this email directly or view it on GitHub
#1.

Qiong
�
Reply to this email directly or view it on GitHub.

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@jiarong @wangqion