[protocols] protocols Digest, Vol 10, Issue 1

Wed Feb 10 16:15:16 PST 2016

Hi Guddu, I'll have to take a look early next week.

best,
--titus

On Wed, Feb 10, 2016 at 09:49:30AM +0200, Guddu Khan wrote:
> Hi,
> I followed the protocol at given link
> http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html
> 
> After running this command
> 
> annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho
> nema.x.mouse.homol
> 
> I got following output as below, Also pasted the first few lines from
> each output file.
> * I used the data given by the author I could not replicate the results can
> you see why ??? *
> (khmerEnv)q at dx4-biotek12:~/Software/Annotation$
> ./eel-pond-master/annotate-seqs.py trinity-nematostella.renamed.fa
> nema.x.mouse.ortho nema.x.mouse.homol
> Scanning sequences -- first pass to gather info
> ... 0
> ... 25000
> ... 50000
> ... 75000
> ... 100000
> ... 125000
> ... 150000
> ... 175000
> ... 200000
> second pass: annotating
> ... x2 0
> ... x2 25000
> ... x2 50000
> ... x2 75000
> ... x2 100000
> ... x2 125000
> ... x2 150000
> ... x2 175000
> ... x2 200000
> ----
> 207533 sequences total
> 0 annotated / ortho
> 0 annotated / homol
> 0 annotated / tr
> 0 total annotated
> 
> annotated sequences in FASTA format: trinity-nematostella.renamed.fa.annot
> annotation spreadsheet in: trinity-nematostella.renamed.fa.annot.csv
> annotation spreadsheet with sequences (warning: LARGE):
> trinity-nematostella.renamed.fa.annot.large.csv
> 
> 
> 
> 
> *less*
> *trinity-nematostella.renamed.fa.annot*>nema.id1.tr89018
> 1_of_1_in_tr89018 len=261 id=1 tr=89018
> CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG
> >nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575
> GCCAGTTGCAAACACGAATTTCAATCCATTAACATTTCATGAGTTGGAATCTCCACAGAAACTTTCTTTTCATCACGACCCCTGTTCCAAATGATTCCTTTCACACAAAACTGACCGGACAGGAAACAGAAAAAACAAGCAAGGGTCATGCAATAGACGACTTATTACCGGAAACCGCGATATTTAGCCAAGACATAAGTGCAAATTAAAACATCGA
> >nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232
> 
> 
> 
> *less trinity-nematostella.renamed.fa.annot.csv*
> sequence name,unique ID,Transcript family,ortholog,homology
> score,homolog,family orthology,family homology,additional information
> nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
> 1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,
> nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2
> tr=459575,id2,tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,,,,,,
> nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3
> tr=219232,id3,tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,,,,,,
> nema.id4.tr355712 1_of_1_in_tr355712 len=226 id=4
> tr=355712,id4,tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,,,,,,
> nema.id5.tr222444 1_of_1_in_tr222444 len=252 id=5
> tr=222444,id5,tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,,,,,,
> 
> *less trinity-nematostella.renamed.fa.annot.large.csv*
> sequence name,unique ID,Transcript family,ortholog,homology
> score,homolog,family orthology,family homology,additional
> information,sequence
> nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
> 1_of_1_in_tr89018 len=261 id=1
> tr=89018,,,,,,,CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG
> 
> On Tue, Feb 9, 2016 at 10:00 PM, <protocols-request at lists.idyll.org> wrote:
> 
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> > Today's Topics:
> >
> >    1. annotate-seqs.py Gives not hit (Guddu Khan)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 9 Feb 2016 17:54:05 +0200
> > From: Guddu Khan <gudduport at gmail.com>
> > Subject: [protocols] annotate-seqs.py Gives not hit
> > To: protocols at lists.idyll.org
> > Message-ID:
> >         <
> > CA+QNwoAXa7pnqj4_LosPJwPV+neZbwMXhtuy_XMjSeoY1T4mUg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> > I followed the protocol in given link
> >
> > http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html
> >
> > After running this command
> >
> > annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho
> > nema.x.mouse.homol
> >
> > I got following output as below, Also pasted the first few lines from
> > each output file.
> >
> > (khmerEnv)q at dx4-biotek12:~/Software/Annotation$
> > ./eel-pond-master/annotate-seqs.py trinity-nematostella.renamed.fa
> > nema.x.mouse.ortho nema.x.mouse.homol
> > Scanning sequences -- first pass to gather info
> > ... 0
> > ... 25000
> > ... 50000
> > ... 75000
> > ... 100000
> > ... 125000
> > ... 150000
> > ... 175000
> > ... 200000
> > second pass: annotating
> > ... x2 0
> > ... x2 25000
> > ... x2 50000
> > ... x2 75000
> > ... x2 100000
> > ... x2 125000
> > ... x2 150000
> > ... x2 175000
> > ... x2 200000
> > ----
> > 207533 sequences total
> > 0 annotated / ortho
> > 0 annotated / homol
> > 0 annotated / tr
> > 0 total annotated
> >
> > annotated sequences in FASTA format: trinity-nematostella.renamed.fa.annot
> > annotation spreadsheet in: trinity-nematostella.renamed.fa.annot.csv
> > annotation spreadsheet with sequences (warning: LARGE):
> > trinity-nematostella.renamed.fa.annot.large.csv
> >
> >
> >
> >
> > *less*
> > *trinity-nematostella.renamed.fa.annot*>nema.id1.tr89018
> > 1_of_1_in_tr89018 len=261 id=1 tr=89018
> >
> > CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG
> > >nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575
> >
> > GCCAGTTGCAAACACGAATTTCAATCCATTAACATTTCATGAGTTGGAATCTCCACAGAAACTTTCTTTTCATCACGACCCCTGTTCCAAATGATTCCTTTCACACAAAACTGACCGGACAGGAAACAGAAAAAACAAGCAAGGGTCATGCAATAGACGACTTATTACCGGAAACCGCGATATTTAGCCAAGACATAAGTGCAAATTAAAACATCGA
> > >nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232
> >
> >
> >
> > *less trinity-nematostella.renamed.fa.annot.csv*
> > sequence name,unique ID,Transcript family,ortholog,homology
> > score,homolog,family orthology,family homology,additional information
> > nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
> > 1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,
> > nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2
> > tr=459575,id2,tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,,,,,,
> > nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3
> > tr=219232,id3,tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,,,,,,
> > nema.id4.tr355712 1_of_1_in_tr355712 len=226 id=4
> > tr=355712,id4,tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,,,,,,
> > nema.id5.tr222444 1_of_1_in_tr222444 len=252 id=5
> > tr=222444,id5,tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,,,,,,
> >
> > *less trinity-nematostella.renamed.fa.annot.large.csv*
> > sequence name,unique ID,Transcript family,ortholog,homology
> > score,homolog,family orthology,family homology,additional
> > information,sequence
> > nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
> > 1_of_1_in_tr89018 len=261 id=1
> >
> > tr=89018,,,,,,,CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG
> >
> >
> >
> >
> > Regards
> >
> > Imran Khan
> > Research Scholar,
> > University of Porto
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-- 
C. Titus Brown, ctbrown at ucdavis.edu