<div dir="ltr">Hi,<br>
I followed the protocol at given link<br>
<a href="http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html" rel="noreferrer" target="_blank">http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html</a><br>
<br>
After running this command<br>
<br>
annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho<br>
nema.x.mouse.homol<br>
<br>
I got following output as below, Also pasted the first few lines from<br>
each output file. <b> I used the data given by the author I could not replicate the results can you see why ???<br>
</b><br>
(khmerEnv)q@dx4-biotek12:~/Software/Annotation$<br>
./eel-pond-master/annotate-seqs.py trinity-nematostella.renamed.fa<br>
nema.x.mouse.ortho nema.x.mouse.homol<br>
Scanning sequences -- first pass to gather info<br>
... 0<br>
... 25000<br>
... 50000<br>
... 75000<br>
... 100000<br>
... 125000<br>
... 150000<br>
... 175000<br>
... 200000<br>
second pass: annotating<br>
... x2 0<br>
... x2 25000<br>
... x2 50000<br>
... x2 75000<br>
... x2 100000<br>
... x2 125000<br>
... x2 150000<br>
... x2 175000<br>
... x2 200000<br>
----<br>
207533 sequences total<br>
0 annotated / ortho<br>
0 annotated / homol<br>
0 annotated / tr<br>
0 total annotated<br>
<br>
annotated sequences in FASTA format: trinity-nematostella.renamed.fa.annot<br>
annotation spreadsheet in: trinity-nematostella.renamed.fa.annot.csv<br>
annotation spreadsheet with sequences (warning: LARGE):<br>
trinity-nematostella.renamed.fa.annot.large.csv<br>
<br>
<br>
<br>
<br>
*less*<br>
*trinity-nematostella.renamed.fa.annot*>nema.id1.tr89018<br>
1_of_1_in_tr89018 len=261 id=1 tr=89018<br>
CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG<br>
>nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575<br>
GCCAGTTGCAAACACGAATTTCAATCCATTAACATTTCATGAGTTGGAATCTCCACAGAAACTTTCTTTTCATCACGACCCCTGTTCCAAATGATTCCTTTCACACAAAACTGACCGGACAGGAAACAGAAAAAACAAGCAAGGGTCATGCAATAGACGACTTATTACCGGAAACCGCGATATTTAGCCAAGACATAAGTGCAAATTAAAACATCGA<br>
>nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232<br>
<br>
<br>
<br>
*less trinity-nematostella.renamed.fa.annot.csv*<br>
sequence name,unique ID,Transcript family,ortholog,homology<br>
score,homolog,family orthology,family homology,additional information<br>
nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018<br>
1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,<br>
nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2<br>
tr=459575,id2,tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,,,,,,<br>
nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3<br>
tr=219232,id3,tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,,,,,,<br>
nema.id4.tr355712 1_of_1_in_tr355712 len=226 id=4<br>
tr=355712,id4,tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,,,,,,<br>
nema.id5.tr222444 1_of_1_in_tr222444 len=252 id=5<br>
tr=222444,id5,tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,,,,,,<br>
<br>
*less trinity-nematostella.renamed.fa.annot.large.csv*<br>
sequence name,unique ID,Transcript family,ortholog,homology<br>
score,homolog,family orthology,family homology,additional<br>
information,sequence<br>
nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018<br>
1_of_1_in_tr89018 len=261 id=1<br>
tr=89018,,,,,,,CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Feb 9, 2016 at 10:00 PM, <span dir="ltr"><<a href="mailto:protocols-request@lists.idyll.org" target="_blank">protocols-request@lists.idyll.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send protocols mailing list submissions to<br>
<a href="mailto:protocols@lists.idyll.org">protocols@lists.idyll.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.idyll.org/listinfo/protocols" rel="noreferrer" target="_blank">http://lists.idyll.org/listinfo/protocols</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:protocols-request@lists.idyll.org">protocols-request@lists.idyll.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:protocols-owner@lists.idyll.org">protocols-owner@lists.idyll.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of protocols digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. annotate-seqs.py Gives not hit (Guddu Khan)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 9 Feb 2016 17:54:05 +0200<br>
From: Guddu Khan <<a href="mailto:gudduport@gmail.com">gudduport@gmail.com</a>><br>
Subject: [protocols] annotate-seqs.py Gives not hit<br>
To: <a href="mailto:protocols@lists.idyll.org">protocols@lists.idyll.org</a><br>
Message-ID:<br>
<<a href="mailto:CA%2BQNwoAXa7pnqj4_LosPJwPV%2BneZbwMXhtuy_XMjSeoY1T4mUg@mail.gmail.com">CA+QNwoAXa7pnqj4_LosPJwPV+neZbwMXhtuy_XMjSeoY1T4mUg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
I followed the protocol in given link<br>
<a href="http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html" rel="noreferrer" target="_blank">http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html</a><br>
<br>
After running this command<br>
<br>
annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho<br>
nema.x.mouse.homol<br>
<br>
I got following output as below, Also pasted the first few lines from<br>
each output file.<br>
<br>
(khmerEnv)q@dx4-biotek12:~/Software/Annotation$<br>
./eel-pond-master/annotate-seqs.py trinity-nematostella.renamed.fa<br>
nema.x.mouse.ortho nema.x.mouse.homol<br>
Scanning sequences -- first pass to gather info<br>
... 0<br>
... 25000<br>
... 50000<br>
... 75000<br>
... 100000<br>
... 125000<br>
... 150000<br>
... 175000<br>
... 200000<br>
second pass: annotating<br>
... x2 0<br>
... x2 25000<br>
... x2 50000<br>
... x2 75000<br>
... x2 100000<br>
... x2 125000<br>
... x2 150000<br>
... x2 175000<br>
... x2 200000<br>
----<br>
207533 sequences total<br>
0 annotated / ortho<br>
0 annotated / homol<br>
0 annotated / tr<br>
0 total annotated<br>
<br>
annotated sequences in FASTA format: trinity-nematostella.renamed.fa.annot<br>
annotation spreadsheet in: trinity-nematostella.renamed.fa.annot.csv<br>
annotation spreadsheet with sequences (warning: LARGE):<br>
trinity-nematostella.renamed.fa.annot.large.csv<br>
<br>
<br>
<br>
<br>
*less*<br>
*trinity-nematostella.renamed.fa.annot*>nema.id1.tr89018<br>
1_of_1_in_tr89018 len=261 id=1 tr=89018<br>
CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG<br>
>nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575<br>
GCCAGTTGCAAACACGAATTTCAATCCATTAACATTTCATGAGTTGGAATCTCCACAGAAACTTTCTTTTCATCACGACCCCTGTTCCAAATGATTCCTTTCACACAAAACTGACCGGACAGGAAACAGAAAAAACAAGCAAGGGTCATGCAATAGACGACTTATTACCGGAAACCGCGATATTTAGCCAAGACATAAGTGCAAATTAAAACATCGA<br>
>nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232<br>
<br>
<br>
<br>
*less trinity-nematostella.renamed.fa.annot.csv*<br>
sequence name,unique ID,Transcript family,ortholog,homology<br>
score,homolog,family orthology,family homology,additional information<br>
nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018<br>
1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,<br>
nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2<br>
tr=459575,id2,tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,,,,,,<br>
nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3<br>
tr=219232,id3,tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,,,,,,<br>
nema.id4.tr355712 1_of_1_in_tr355712 len=226 id=4<br>
tr=355712,id4,tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,,,,,,<br>
nema.id5.tr222444 1_of_1_in_tr222444 len=252 id=5<br>
tr=222444,id5,tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,,,,,,<br>
<br>
*less trinity-nematostella.renamed.fa.annot.large.csv*<br>
sequence name,unique ID,Transcript family,ortholog,homology<br>
score,homolog,family orthology,family homology,additional<br>
information,sequence<br>
nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018<br>
1_of_1_in_tr89018 len=261 id=1<br>
tr=89018,,,,,,,CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG<br>
<br>
<br>
<br>
<br>
Regards<br>
<br>
Imran Khan<br>
Research Scholar,<br>
University of Porto<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.idyll.org/pipermail/protocols/attachments/20160209/105e7331/attachment-0001.htm" rel="noreferrer" target="_blank">http://lists.idyll.org/pipermail/protocols/attachments/20160209/105e7331/attachment-0001.htm</a>><br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
protocols mailing list<br>
<a href="mailto:protocols@lists.idyll.org">protocols@lists.idyll.org</a><br>
<a href="http://lists.idyll.org/listinfo/protocols" rel="noreferrer" target="_blank">http://lists.idyll.org/listinfo/protocols</a><br>
<br>
<br>
End of protocols Digest, Vol 10, Issue 1<br>
****************************************<br>
</blockquote></div><br></div>