User: HZZ0036

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HZZ00360
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Posts by HZZ0036

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Error about Count_fasta.pl
... Thank you. It worked for a subset of the file, but it still didn't work for all of the file. I didn't meet this situation before. It's very strange. ...
written 10 days ago by HZZ00360
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Comment: C: Error about Count_fasta.pl
... I can't find the error for fasta file. Here is the file link: https://filemover.auburn.edu/files/files/1510608526_re69allokay.fa Could you please have a look? How to check if it is formatted correctly? Thank you so much. ...
written 11 days ago by HZZ00360
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Error about Count_fasta.pl
... Hello Everyone, I tried to use the Count_fasta.pl script (https://github.com/sr320/eimd/blob/master/scripts/count_fasta.pl) to get the N50 for one assembled fasta file. However, when I ran *perl Count_fasta.pl file.fa* ,it showed: 0:99 0 Total length of sequence: 0 bp To ...
assembly sequencing written 11 days ago by HZZ00360
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Comment: C: MCScanX result problem
... Hi, I have solved this problem, but I got a very strange circle. Could you please see the new post: https://www.biostars.org/p/276418/ Thanks. ...
written 7 weeks ago by HZZ00360
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Very strange circle from MCScanX
... Hi, I am using MCScanX to compare maize genome and my draft plant genome, which only have scaffolds. I used circle_plotter.java got a very strange circle since I put all of the my scaffolds number in the control_file. How to deal with this like one species have no chromosomes, only have scaff numbe ...
genome sequence written 7 weeks ago by HZZ00360 • updated 7 weeks ago by Philipp Bayer4.8k
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Comment: C: MCScanX result problem
... Thanks. I have tried, but it still doesn't work. The log file showed: Reading BLAST file and pre-processing Generating BLAST list 0 matches imported (7239387 discarded) 0 pairwise comparisons 0 alignments generated Pairwise collinear blocks written to /mcScanX_gg_maize_analy ...
written 8 weeks ago by HZZ00360
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Comment: C: MCScanX result problem
... Here is the script for blastall: blastp -db /mcScanX/goose_maize -query /mcScanX/goose_maize.fa -out /mcScanX/goose_maize.blast -evalue 1e-10 -outfmt 6 -num_threads 20 -num_alignments 5 ...
written 9 weeks ago by HZZ00360
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Comment: C: MCScanX result problem
... I have removed it from blast output. Now the gene name in gff file and blast output file is same, but it still doesn't work. Could you please have a look again? Here is the link: https://filemover.auburn.edu/files/files/1505917638_goosemaize.blast https://filemover.auburn.edu/files/files/1505917678 ...
written 9 weeks ago by HZZ00360
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Comment: C: MCScanX result problem
... My draft genome has no chr name, only scaffold name. I creat a link for .blast and .gff files. Could you please have a look? Thanks. https://filemover.auburn.edu/files/files/1505337598_goosemaize.blast https://filemover.auburn.edu/files/files/1505337635_goosemaize.gff ...
written 10 weeks ago by HZZ00360
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MCScanX result problem
... Hello, I want to use MCScanX to see the synteny blocks for my weed draft genome and maize genome. I downloaded maize genome from NCBI. Then I prepared .blast and .gff file and run ./MCScanX according to the manual, however, in the collinearity result file, it showed: ############### Parameters ...
genome sequence written 10 weeks ago by HZZ00360 • updated 10 weeks ago by kashifalikhan00740

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