User: Darill

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Darill20
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Posts by Darill

<prev • 92 results • page 1 of 10 • next >
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What kind of protein matrix substitution use for blastX divergent sequences
... I'm actually trying to find some homology between sequences inside a genome and several viral proteins in a database. As you all know, virus evolve very quickly, so I'm expecting to find a lot a divergences between the sequences I compared. In the literature I see that BLOSUM < 62 are used for ...
matrix homology diamond blast written 6 weeks ago by Darill20
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Comment: C: output path issue on Busco (python)
... Yep it works if I modify it directly in the config.ini file of course but the output path will change depending on the script I use... I have around 100 script to run with a unique path for each job, that is why I want to incorporate the out_path directly in my script and not in the config.ini whi ...
written 9 weeks ago by Darill20
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Comment: C: output path issue on Busco (python)
... Yes I removed the ; part but there is still the same issue. ...
written 9 weeks ago by Darill20
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Comment: A: Recover fasta sequences in database from the blast output 6
... Hi everyone, I have some news concerning the idea you proposed me. The issue is in term on time because if I write a command line for each hit blast, it is about `310 000` commande lines to execute in order to recover the fasta sequences in the database corresponding to the range start and end. So ...
written 10 weeks ago by Darill20
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Comment: C: Recover fasta sequences in database from the blast output 6
... I get error messages such as: IDBA_scaffold_10046632436: 1: IDBA_scaffold_10046632436: Syntax error: Unterminated quoted string IDBA_scaffold_2263239172667: 1: IDBA_scaffold_2263239172667: Syntax error: Unterminated quoted string IDBA_scaffold_2469820637: 1: IDBA_scaffold_2469820637: S ...
written 10 weeks ago by Darill20
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Comment: C: Recover fasta sequences in database from the blast output 6
... I'm not sure to understand what you mean by `duplicate`, here is an exemple of the blast output : YP_006347591.1 IDBA_scaffold_19039 30.319 188 119 6 1772 1953 1083 1628 8.97e-24 80.5 YP_006347591.1 IDBA_scaffold_19039 37.500 88 54 1 1652 1738 712 975 8.97e-24 54.7 YP_006347732.1 IDBA_scaf ...
written 10 weeks ago by Darill20
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Comment: C: Recover fasta sequences in database from the blast output 6
... Ok but if in the -entry there is only the ID, where is the file `blast_lh_all_new.out` where are available the coordinates "end and start" ...
written 10 weeks ago by Darill20
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Comment: C: Recover fasta sequences in database from the blast output 6
... Hi, thanks for your answer. Since the ID of my database are in the column 2 should I not cut the column 2 instead and do : awk '{print $2 $9 $10}' blast_lh_all.out > blast_lh_all_new.out With in the blast_lh_all_new.out in the column 1 the ID of the hit blast in my database and une the 2 ...
written 10 weeks ago by Darill20
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Recover fasta sequences in database from the blast output 6
... Hello everyone, I made a blast research and I got the output in the table format 6. So I got several hits and I would like to retrieve each fasta sequences from the blast database with the start and end corresponding of the hit. I saw that that the command `blastdbcmd` should be able do to the tr ...
fasta blast output written 10 weeks ago by Darill20
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Comment: C: Issue using IDBA
... OK sorry for that, here are the file contents of .error and .out: more ACG-006_assembly.error /var/spool/torque/mom_priv/jobs/15583407.SC: line 28: 30378 Killed $IDBA'bi n/idba_ud' --pre_correction -o /pandata/LEPIWASP/ACG-0006_0027/OUT-0006-2 -r $INPUT1'.fa' --num_thr ...
written 7 months ago by Darill20

Latest awards to Darill

Great Question 8 weeks ago, created a question with more than 5,000 views. For compare 2 dataframe with pandas
Great Question 4 months ago, created a question with more than 5,000 views. For C extension: No module named 'pandas._libs.tslib' not built (pandas)
Popular Question 6 months ago, created a question with more than 1,000 views. For compare 2 dataframe with pandas
Popular Question 8 months ago, created a question with more than 1,000 views. For compare 2 dataframe with pandas
Popular Question 8 months ago, created a question with more than 1,000 views. For C extension: No module named 'pandas._libs.tslib' not built (pandas)
Rising Star 10 months ago, created 50 posts within first three months of joining.

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