User: yifangt86

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yifangt8610
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USA
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19 hours ago
Joined:
5 years, 11 months ago
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Posts by yifangt86

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Half missing genotype in *.ped files
... It seems to me your SNP identifiers are not consistent creating the problem. Likely some thing happened with Line 2, 3, 4, 5 to have space in the string, I guess. Replace the space with underscore (_) or, simply remove the spaces to have another try. ...
written 6 days ago by yifangt8610
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Answer: A: How to ensure sequential execution of rules in Snakefile one after another?
... Just found the source to **handle sequential execution** as **[Rule dependencies][1]**. Leave it here for reference, if it is not annoying. > From verion 2.4.8 on, rules can also refer to the output of other > rules in the Snakefile, e.g.: > > rule a: > input: "path/to ...
written 28 days ago by yifangt8610
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Comment: C: How to ensure sequential execution of rules in Snakefile one after another?
... Thanks! Could you please elaborate more of this line to ensure the completion of **trimming** before **fastqc_trimmed** starts? rule fastqc_trimmed: input: inputFiles = expand(...), trimmedFiles = rules.trimming.output.fwd_paired outpu ...
written 29 days ago by yifangt8610
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How to ensure sequential execution of rules in Snakefile one after another?
... Hello, I was struggling for a while about the execution of Snakefile rules. I have a scenario that some rules must be completed before the next one starts because of the dependency, especially when parallel processes are used with the **-j option**. I met this situation when the sample sizes are ve ...
snakefile execution completion written 29 days ago by yifangt8610
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Comment: C: karyoploteR: uncircle your genomes
... Hello Bernat! I still have problem to create the "**data=regions**" object for kpPlotCoverage(kp, data=regions) I have exactly same dataframe in bed file format like Vijay's example above: test=read.csv("test", sep="\t", stringsAsFactors = F, strip.white = T) If I understand correctl ...
written 11 weeks ago by yifangt8610
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Comment: C: Extracting allele, Genotype from VCF file
... Hi finswimmer! Can I ask for the trick to convert the output to symbolic genotypes? for your example: chr1 10177 ACC ACCC ACC/ACCC chr1 10327 T C T/T chr1 10352 TAC TAAC TAAC/TAAC chr1 12783 G A A/A Searched for a whole, but just did not have my luck. ...
written 6 months ago by yifangt8610
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Comment: C: Approaches to generate various phylogenetic tree topologies (Chained, balanced a
... I was looking for the opposite direction to convert newick file to the distance matrix. Too many packages on phylogenetics, but it seems there is no straight answer for non-phylogeneticist like me. ...
written 18 months ago by yifangt8610
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Rcircos for Multiple tracks of Expression data
... Hello I am trying to plot expression data with Rcircos without an ideogram information. My dataframe is like this: Chr Start End Band CSR1 CSR2 CSR3 MTR1 MTR2 MTR3 chr5B 16521 20994 AeCS5B01G000100 1821.8 739.6 1234.0 1146.2 1380.0 1229.4 chr5B 60616 61023 AeCS5B01G000200 104.2 6 ...
expression data ideogram rcircos multiple tracks written 21 months ago by yifangt8610
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Answer: A: transcripts sequence preparation for RNAseq DE analysis
... Thanks genomax and h.mon! I found out the solution for my problem with [**gffread**][1], and I post it here for those who have the same problem. gffread $gff3_file -g $genome.fasta -w transcripts.fasta -w write a fasta file with spliced exons for each GFF transcript #So that th ...
written 21 months ago by yifangt8610
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Comment: C: transcripts sequence preparation for RNAseq DE analysis
... Thanks! Kallisto manual indicates to use transcripts for index. Could you please share your idea to get transcript-level / gene-level from the indexed whole genome, if possible? Thanks again. ...
written 21 months ago by yifangt8610

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Popular Question 5 months ago, created a question with more than 1,000 views. For How is the FM-index built for multiple entries of a fasta file?

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