User: MAPK

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MAPK1.2k
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Posts by MAPK

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Answer: A: Alternate colors in R based on a factor value
... You could simply use `col = your-factors` option for your factor. What's your factor here? Try something like this: https://stackoverflow.com/questions/7721262/colouring-plot-by-factor-in-r ...
written 17 days ago by MAPK1.2k
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(Closed) How to count positively and negatively aligned reads in a bam file?
... I have a bam file and I would like to count the number of plus and minus strand aligned tothe reference sequence. How can I get this data from a bam file? Thanks for your help in advance. ...
bam written 7 weeks ago by MAPK1.2k
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How to run microsynteny plotter from McScan?
... I was trying to run microsynteny of Madbox gene family using the McScan tool's `family_circle_plotter.java` available here (https://github.com/wyp1125/MCScanX/blob/master/downstream_analyses/family_circle_plotter.java ). I followed the manual (http://chibba.pgml.uga.edu/mcscan2/documentation/manua ...
microsynteny mcscan written 8 weeks ago by MAPK1.2k • updated 10 days ago by annapragada.harika0
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Comment: C: Java code for dual_synteny_plot from MCscanx generating error
... Thank you for your answer. Now I am getting this error: java dual_synteny_plotter -g xyz.gff -s xyz.collinearity -c at_vv_dual_syn.ctl -o output_png.png Reading control file error: For input string: "200 //plot width (in pixels)" Exception in thread "main" java.lang.IllegalArgumentExce ...
written 9 weeks ago by MAPK1.2k
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Java code for dual_synteny_plot from MCscanx generating error
... I am running the program called dual_synteny_plotter from MCScanx (https://github.com/wyp1125/MCScanX/blob/master/downstream_analyses/dual_synteny_plotter.java) like this: `dual_synteny_plotter.java -g xyz.gff -s xyz.collinearity -c at_vv_dual_syn.ctl -o output_png.png`. This generates error message ...
synteny written 9 weeks ago by MAPK1.2k • updated 9 weeks ago by Pierre Lindenbaum107k
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Comment: C: Nanopore data and downstream anlysis
... Ok. Thank you. No this is new data. I also have two directories with both multiple fast5 and one fastq files for each microbiome sample. Should I use the fastq file generated by live basecalling method or should I convert all fast5 files to fastq? ...
written 9 weeks ago by MAPK1.2k
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Comment: C: Nanopore data and downstream anlysis
... Thank you so much for your answer. Yes the base calling was done using live basecalling method. Now I have some more questions: 1. Would you suggest to concatenate all the fasta reads extracted from fast5 files from all subdirectories? 2. Do I need to separate 1D and 2D reads and what type of reads ...
written 9 weeks ago by MAPK1.2k
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Nanopore data and downstream anlysis
... I have a few microbiome data sequenced with Nanopore Minion. For each run, I have **pass**, **fail** and **skip** directories. Within the **pass** directory, I also have 0:10 (10 different) subdirectories. Would someone please explain me the difference between **pass**, **fail** and **skip** data a ...
nanopore written 9 weeks ago by MAPK1.2k • updated 9 weeks ago by WouterDeCoster28k
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How to run microsynteny using MCscan?
... I have been trying to run microsynteny for a set of MAPK genes from two plant species using http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf. I have protein sequences of MAPK gene from Arabidopsis and Sunflower. I also have gff file for both genomes including their genome sequences. Can s ...
mcscan written 9 weeks ago by MAPK1.2k • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: What cigar to use to count reads with last base mismatch in Rsamtools?
... Thank you. So how do you separate reads with tag NM =1? What tool can I use? ...
written 11 weeks ago by MAPK1.2k

Latest awards to MAPK

Great Question 3 days ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: R programming: string split n number of characters and cbind them in n number of
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to change the SM tags of BAM files
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to change the SM tags of BAM files
Popular Question 9 weeks ago, created a question with more than 1,000 views. For How to change the SM tags of BAM files
Popular Question 9 weeks ago, created a question with more than 1,000 views. For How to change the SM tags of BAM files
Great Question 11 weeks ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to obtain the length of coding regions for the list of genes?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to change the SM tags of BAM files
Popular Question 3 months ago, created a question with more than 1,000 views. For How to change the SM tags of BAM files
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Popular Question 4 months ago, created a question with more than 1,000 views. For How to estimate the power of association test for small sample size
Popular Question 4 months ago, created a question with more than 1,000 views. For Extracting subset of VCF file for list of genes
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Popular Question 4 months ago, created a question with more than 1,000 views. For How to estimate the power of association test for small sample size
Popular Question 4 months ago, created a question with more than 1,000 views. For Command to extract SNPs from VCF file using bcftool
Popular Question 5 months ago, created a question with more than 1,000 views. For Command to extract SNPs from VCF file using bcftool
Popular Question 5 months ago, created a question with more than 1,000 views. For Command to extract SNPs from VCF file using bcftool
Popular Question 5 months ago, created a question with more than 1,000 views. For Command to extract SNPs from VCF file using bcftool
Popular Question 6 months ago, created a question with more than 1,000 views. For Command to extract SNPs from VCF file using bcftool
Scholar 6 months ago, created an answer that has been accepted. For A: R programming: concatenate three character vectors
Popular Question 6 months ago, created a question with more than 1,000 views. For Command to extract SNPs from VCF file using bcftool
Student 7 months ago, asked a question with at least 3 up-votes. For R programming, concatenate or combine all the column contents
Great Question 7 months ago, created a question with more than 5,000 views. For R programming: compare columns to column and get the mismatch

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