User: Bioinformatician_in_trouble

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Posts by Bioinformatician_in_trouble

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Comment: C: Coloring nodes according to attribute value in Cytoscape 3
... hi i have the same issue. How did you solve the problem? ...
written 10 days ago by Bioinformatician_in_trouble0
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Comment: C: Cytoscape: how to show different interactions using different lines or different
... Hi asaf, Thank you for your reply.I am not sure how to add attributes( saw the attribute file format from cytoscape manual, but could not follow) This is how i have placed the columns in the excel sheet that I used to create network Gene 1 Gene 2 Interaction ATM TP53 Activates CHEK1 CDC25 Inhibits ...
written 11 days ago by Bioinformatician_in_trouble0
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Cytoscape: how to show different interactions using different lines or different colors
... Hi All, I am trying to create a network in cytoscape 3.4.0 where my source and target are genes and my interaction would be "activates" or "Inhibits". My question is, I want to show the interactions either by using different line color or different line type. How can I do this. ? Looking forward for ...
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Comment: C: Detection of fusion from a DNA seq file
... Organism: Human I know the genes that are fused. I have a BAM file that contains the DNA sequence. I tried running TOPHAT fusion but it gave zero fusions. I am not sure how to run Breakdancer, as the perl and cpp version is confusing for me, even after reading the tutorial. TIA. ...
written 16 days ago by Bioinformatician_in_trouble0
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Detection of fusion from a DNA seq file
... Hi, Can anyone please suggest some free softwares that could help in detection of fusion from a DNA seq file.? Looking forward for response. Thank you in advance. ...
next-gen written 16 days ago by Bioinformatician_in_trouble0 • updated 16 days ago by Etal1.4k
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Comment: A: MPile up Result contains "X" in Alt column
... Thank you both of you for your reply. @ Devon Ryan: It is a local instance of galaxy. And My output from mpileup is a VCF file, so I am not sure how useful will Bcftools will be. @ Berge2015 :Thank you,I did see these posts.But again,it was on command line. And I am using the web version of galaxy. ...
written 4 months ago by Bioinformatician_in_trouble0
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MPile up Result contains "X" in Alt column
... Hi everyone, I am trying to use mpileup(samtools) for variant calling. In my results which happens to be a VCF file, I get " X" in alt column. The documentation on mpileup says that "In the BCF generated by SAMtools, an non-ref base 'X' represents an base has not been seen from the alignment data. S ...
galaxy samtools mpileup written 4 months ago by Bioinformatician_in_trouble0
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ROD file for GATK's Haplotype Caller
... Hey guys, I wanted to use GATK's HAplotype caller tool in my local instance of GALAXY, however I need to submit a ROD file. Please help me with what is ROD file and where can I obtain it from?My reference genome has been obtained from UCSC genome browser. Waiting for response as I cannot proceed wi ...
next-gen snp written 5 months ago by Bioinformatician_in_trouble0
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Comment: C: BED file creation from UCSC Output
... Well, when I right click on the output page and click on "save as", the only format it saves is in txt. ...
written 5 months ago by Bioinformatician_in_trouble0

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