User: HZZ0036

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HZZ00360
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Posts by HZZ0036

<prev • 19 results • page 1 of 2 • next >
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How to plot Orthofinder results?
... Hi everyone, I ran Orthofinder for six plant genomes and got some results, which include a lot of statistics. I only made a phylogenetic tree for those species, but I don't know how to plot other results? How to use those results to do some gene family analyses? Here is the information from the man ...
genome written 17 days ago by HZZ00360
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(Closed) Sed problem to change names
... Hi, I want to use 'Sed' to change the names in both sequences and annotation files. Such as change scaffold1_size2426064 exon scaffold2_size1571916 exon scaffold3_size1509833 gene scaffold4_size1453470 scaffold5_size1243770 scaffold6_size1253778 scaffold7_size1219719 ...
sequence written 22 days ago by HZZ00360 • updated 22 days ago by Federico Lopez20
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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 3 months 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 3 months 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 3 months 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 4 months 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 4 months ago by HZZ00360 • updated 4 months ago by Philipp Bayer5.2k
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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 5 months 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 5 months 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 5 months ago by HZZ00360

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