User: tcf.hcdg

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tcf.hcdg40
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European Union
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3 days, 8 hours ago
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2 years ago
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Posts by tcf.hcdg

<prev • 82 results • page 1 of 9 • next >
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Comment: C: How to merge BLAST XML output from different database?
... As I mentioned in the previous comment, because fo the GNU parallel each file has multiple blast xml header and footer. I remove the repeated header and footer from the file and then tried your script, it worked and merged two files. But the resultant file in in one line blastx ...
written 10 weeks ago by tcf.hcdg40
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Comment: C: How to merge BLAST XML output from different database?
... I think the script should be like: First it should merge all the resulted xml files that was generated for one database 1 let's say in this case merge all 31 files of database1 Then it should some how sort the xml files. The reason to sort is queries are not insorted format,because I used GNU pa ...
written 10 weeks ago by tcf.hcdg40
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Comment: C: How to merge BLAST XML output from different database?
... I am sorry I couldn't respond earlier because of my limited posting option. Well, Itried and the output is like that: tb44227@lido-gw02:~/nobackup/jvarkit>xmllint ~/nobackup/Radula/Trinity_1500k_Radula_lnr_hededt_split/merging_xml_db1_db2/03_Rma_trn1500k_nrbx5_hsp20_e3_dbp1 > /dev ...
written 10 weeks ago by tcf.hcdg40
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Comment: C: How to merge BLAST XML output from different database?
... java -jar dist/mergeblastxml.jar ~/nobackup/Radula/Trinity_1500k_Radula_lnr_hededt_split/merging_xml_db1_db2/03_Rma_trn1500k_nrbx5_hsp20_e3_dbp1 ~/nobackup/Radula/Trinity_1500k_Radula_lnr_hededt_split/merging_xml_db1_db2/03_Rma_trn1500k_nrbx5_hsp20_e3_dbp2 > output.xml [INFO][MergeBlastX ...
written 10 weeks ago by tcf.hcdg40
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Comment: C: How to merge BLAST XML output from different database?
... No, ecah file has 50000 query sequences, am I have 62 files 31 for each. ...
written 10 weeks ago by tcf.hcdg40
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Comment: C: How to merge BLAST XML output from different database?
... For example "TRINITY_DN99193_c0_g5" query against database1 blastx BLASTX 2.6.0+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation ...
written 10 weeks ago by tcf.hcdg40
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Comment: C: How to merge BLAST XML output from different database?
... Yes I use the same query sequence for both part of database. ...
written 10 weeks ago by tcf.hcdg40
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How to merge BLAST XML output from different database?
... Hello I did the command line BLAST against NCBI nr database. Because of the limited computational resourses, administrator at our university reccomended me to split the query sequence as well as databases (120gb of nr). I splited the database in almost two equall parts and then did the blastx agai ...
blastxml merge blast written 10 weeks ago by tcf.hcdg40 • updated 10 weeks ago by Pierre Lindenbaum95k
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How to run Interproscan with old GLIBC 2.12 on centos cluster?
... Hello I would like to run interproscan on cluster through PBS /torque. I tried wtih the test script and could not succeed because of the GLIBC_2.14. The reason is the entire software stack of CentOS 6.8 which our cluster is running was built on top of glibc 2.12 which at the moment can't be upg ...
cluster interproscan written 3 months ago by tcf.hcdg40 • updated 9 weeks ago by Michael Dondrup42k
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Comment: C: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
... got it. my mistake. Now worked ...
written 5 months ago by tcf.hcdg40

Latest awards to tcf.hcdg

Popular Question 4 weeks ago, created a question with more than 1,000 views. For standalone blast , database error
Popular Question 4 months ago, created a question with more than 1,000 views. For standalone blast , database error
Popular Question 8 months ago, created a question with more than 1,000 views. For unique sequence IDs from fasta file

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