User: s.kyungyong64

gravatar for s.kyungyong64
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Location:
Berkeley, USA
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3 months, 3 weeks ago
Joined:
3 years, 4 months ago
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Posts by s.kyungyong64

<prev • 25 results • page 1 of 3 • next >
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Answer: A: SNAP error in MAKER exon:out_of_bounds
... Did you solve this problem? I have not encountered any problems when training SNAP with MAKER outputs. But when training SNAP for other matters, the out_of_bounds issue occurred to me when the the fasta headers are not listed in the same order in both genome.ann and genome.dna. less genome.ann ...
written 5 months ago by s.kyungyong6430
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Comment: C: clustering from the minimum distance
... I found out I was supposed to use hclust instead of hcluster :( ...
written 12 months ago by s.kyungyong6430
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clustering from the minimum distance
... Hi all, I have the following distance matrix which is a direct output of some pairwise sequence metric. > as.dist(df) 0 1 2 3 4 5 6 7 8 1 1.9356 2 1.6758 2.8880 ...
R clustering written 12 months ago by s.kyungyong6430
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RNAseq Tximport transcript counts to gene counts
... Hi! I have quant.sf files generated by Salmon by mapping 100bp single-end Illumina libraries against primary transcripts. The genome for this species is not so perfect and is missing some genes of interest. So I am using both transcriptome and genome data for this RNA-seq. Before passing this qu ...
tximport salmon rna-seq written 2.1 years ago by s.kyungyong6430 • updated 2.1 years ago by h.mon30k
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Comment: C: FALCON error while running
... It seems lfs isn't required. I guess my problem was the PATH variable as Kevin said. I set up virtualenv and the paths. Everything worked out fine. ...
written 2.6 years ago by s.kyungyong6430
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Comment: A: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Thanks Roxane! I am about to polish my contigs, and your post is really helpful! My pacbio reads have primer sequences at the both ends of reads ( ~ 60nt). So I ended up having to generate the CCS reads, trim the adapters and assemble it with Canu. But since I can't modify the sam file of subreads ...
written 2.7 years ago by s.kyungyong6430
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Merging two split contigs
... Hi all, I have contigs assembled by Canu. While annotating the contigs, I realized that contig A and contig B are actually continuous but split as two different contigs. The end of contig A is overlapping with the end of contig B with 100% ID over a significant length. contigA >... ...
assembly alignment written 2.7 years ago by s.kyungyong6430 • updated 2.7 years ago by maxwhjohn1988100
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Comment: C: SMRT Analysis installation problem - no smrtpipe.py
... It does not return anything :( ...
written 2.9 years ago by s.kyungyong6430
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FALCON error while running
... Hi, all. I am trying to run FALCON on my Mac, but there seems to be problems... :FALCON_2_trial $ fc_run.py fc_run.cfg [9620]$('lfs setstripe -c 12 /Users/Desktop/Heinz/FALCON_2_trial') sh: lfs: command not found [9620]WARNING: Call 'lfs setstripe -c 12 /Users/Desktop/Heinz/FALCON_2 ...
falcon written 2.9 years ago by s.kyungyong6430 • updated 2.2 years ago by 13489881930
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Comment: C: FALCON installation: Command "python setup.py egg_info" failed with error code 1
... Ah, Thank you! It worked with easy_install! sudo easy_install networkx sudo su make -j all ...
written 2.9 years ago by s.kyungyong6430

Latest awards to s.kyungyong64

Popular Question 11 months ago, created a question with more than 1,000 views. For FALCON error while running
Popular Question 2.1 years ago, created a question with more than 1,000 views. For FALCON error while running
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Choosing de novo genome assembly
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Getting PFAM database
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Trimming out primer sequences in the middle of reads
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Has anyone run Phobius locally? Error - could not read provided fasta sequences
Popular Question 2.5 years ago, created a question with more than 1,000 views. For FALCON installation: Command "python setup.py egg_info" failed with error code 1
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Getting PFAM database

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