User: kuick77

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kuick7710
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Posts by kuick77

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Extract depth coverage of a particular region from BAM file
... I tried a simple method to achieve what i wanted, because personally I am not a bioinformatician. What I did was: 1: Load the BAM file into IGV ![screen shot][1] 2: Check "Show Splice Junction Track" 3. Right Click the splicing junction and click "Export Features" in bed file 4. Load the Bed fil ...
written 10 months ago by kuick7710
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Answer: A: Extract depth coverage of a particular region from BAM file
... Hi Jen, Thanks very much. [screen shot][1] I attached the scenario. I tried HTseq-count, but it requires a GFF file, I do not know about how to get it in order to complete the analysis. ![Screen Shot][2] [1]: https://s31.postimg.org/cb9l9awdn/2016_06_26.png [2]: https://postimg.org/image/ ...
written 10 months ago by kuick7710
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Extract depth coverage of a particular region from BAM file
... Hi, If any kind soul could help, I loaded BAM files in IGV and i notice some interesting splicing junction read depth across my samples. I am currently manual click the location in order to view the depth. Is there a method to do that automatically to look at all junction coverage? I am working on ...
bam written 10 months ago by kuick7710
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Comment: C: How to put 2 reference choromosomes in one file so that i can perform alignment
... I just use the h19 genome reference instead, though it takes slower. THanks ...
written 10 months ago by kuick7710
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How to put 2 reference choromosomes in one file so that i can perform alignment based on only these 2?
... Hi There, Just a quick question, I am trying to perform alignment for three of my target genes located in chr 2 and chr3. I uploaded these two reference genome separately. I realised the alignment only allow me to put one reference per analysis. So i created two BAM files from one dataset. I have ...
alignment written 10 months ago by kuick7710
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intron retention analysis
... Hi! I am hoping to use the analysis tools that are available in Galaxy to achieve my tasks. I am running target seq (illumina) with primers targeting only exon-exon junctions e.g. 1-2, 2-3, 3-4.. I am studying 1) exon skipping* and 2) intron retention of my sample. I have run the usual RNA-Seq an ...
galaxy tophat written 11 months ago by kuick7710
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Comment: C: To varscan mpileup data
... Hi Bryantl, The galaxy was down yesterday, but i checked this morning and it was a miracle!!! Thanks so much! Have a nice day! ...
written 11 months ago by kuick7710
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Comment: C: To varscan mpileup data
... Yes bryantl and thanks for your reply. It generated two files, one is vcf , another is log file (both shown in green). I can view the vcf file in the galaxy. But when I proceed to use Varscan, there is no option for me to pick this vcf file.. I am puzzled. ...
written 11 months ago by kuick7710
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To varscan mpileup data
... HI, I have run the mpileup (process is completed and successful), and was trying to analyse the pile up data using Varscan, but why i didnt see any pileup dataset for me to choose in Varscan analysis tool? ...
tophat written 11 months ago by kuick7710 • updated 11 months ago by Jennifer Hillman Jackson22k

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