User: jvire1

gravatar for jvire1
jvire110
Reputation:
10
Status:
New User
Location:
Last seen:
4 days, 18 hours ago
Joined:
6 months, 2 weeks ago
Email:
j*****@cub.uca.edu

Posts by jvire1

<prev • 15 results • page 1 of 2 • next >
0
votes
5
answers
239
views
5
answers
Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... Thank you so much! This worked and I was impressed how fast it processed everything. I am still going to see if I can get the solution in python, because I will likely need to be able to do similar tasks and it would be nice to know how to do it myself. Here is the output: NF-YA NF-YA ...
written 7 days ago by jvire110
0
votes
5
answers
239
views
5
answers
Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... Thank you for all your help. Here is three FASTA entries in the PlantTFDB FASTA file, with the first one corresponding to the first accession ID in the acc_list.txt: >Zpz_sc04830.1.g00020.1.sm.mk Zoysia pacifica|NF-YA|NF-YA family protein MEAKFFRFLKLVGVGFKARSESQGRELFLKLGYSHEVLFTAPPAVRVFC ...
written 7 days ago by jvire110
0
votes
5
answers
239
views
5
answers
Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... Thank you for this awk approach, unfortunately I am needing each line in the accession to be searched one at a time against the FASTA database, retaining duplicate instances. The idea here was to take the accessions and get back the gene name for each. For example an acc.txt file that looked like th ...
written 7 days ago by jvire110
0
votes
1
answer
120
views
1
answers
Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Thank you, that is much cleaner. ...
written 7 days ago by jvire110
0
votes
1
answer
120
views
1
answers
Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Thank you so much for this one liner and to all those who helped. Combined these scripts have allowed me to achieve my goal: Bhlh 533 Myb_Related 397 C2H2 355 Nac 352 C3H 337 Erf 297 Myb 265 Wrky 263 B3 249 Bzip 217 Far1 196 G2-Like 167 Gras 157 ...
written 7 days ago by jvire110
0
votes
1
answer
120
views
1
answers
Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Finally LibreOffice unfroze (wish I could force it to use all 4 cpu)! Here is an example of the columns: PlantTFDB_ALL_TF_pep_BLASTX PlantTFDB_ALL_TF_pep_BLASTP Zpz_sc04830.1.g00020.1.sm.mk^Zpz_sc04830.1.g00020.1.sm.mk^Q:488-228,H:5-93^44.94%ID^E:6e-15^.^. Zpz_sc04830.1.g00020.1.sm.mk^Zpz_ ...
written 7 days ago by jvire110
0
votes
1
answer
120
views
1
answers
Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Sure, LibreOffice is frozen at the moment the two columns are TAB delimited and the annotations within are delimited with '^'. The identifier I need is the one before the first ^, however my plan was to take the new list of annotations and open in LibreOffice, specifying it as '^' delimited and then ...
written 7 days ago by jvire110
3
votes
1
answer
120
views
1
answer
Combining two columns in a tab-delimited file where there is a zero in one
... Hi all, I am currently trying to fill in annotations from a BLASTP of the same database into rows that are 0 in the BLASTX. The columns look like this: BLASTX BLASTP annot1 annot1 annot 2 0 0 annot3 In this example I want "annot3" to be moved under the BLASTX c ...
rna-seq written 7 days ago by jvire110 • updated 7 days ago by kashifalikhan00740
0
votes
5
answers
239
views
5
answers
Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... After I looked at the output more closely I realized that it isn't doing quite what I want it to. The beginning of the list of identifiers looks like this: Zpz_sc04830.1.g00020.1.sm.mk Zpz_sc04830.1.g00020.1.sm.mk Zpz_sc04830.1.g00020.1.sm.mk Zpz_sc04830.1.g00020.1.sm.mk Zpz_s ...
written 8 days ago by jvire110
9
votes
5
answers
239
views
8 follow
5
answers
Pulling out gene names from a FASTA file with a list of IDs
... Does anyone know of a simple scripting solution to take a list of accessions and pull out the gene name from the header of FASTA sequences? For instance given the accession: XP_016469325.1 and given the FASTA entry: >XP_016469325.1 Nicotiana tabacum|C3H|C3H family protein MEEELLKRNTDCVYFLASPLTC ...
rna-seq written 8 days ago by jvire110 • updated 7 days ago by cpad01121.9k

Latest awards to jvire1

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1393 users visited in the last hour