User: lnaren

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lnaren10
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10
Status:
New User
Location:
Canada
Last seen:
3 months ago
Joined:
2 years, 11 months ago
Email:
l*****@hotmail.com

Posts by lnaren

<prev • 13 results • page 1 of 2 • next >
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Irreproducible discovery rate (IDR)
... Hello, I was trying to measure the reproducibility of the 3 set of peaks identified from three replicates. And noticing the "Irreproducible discovery rate (IDR)" maybe only suitable for 2 sets of peaks. Just wondering are there any similar analysis available in Galaxy could check the reproducibilit ...
chip-seq written 3 months ago by lnaren10
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Differentiate data between two heatmap data sets
... Hello, I had Bowtie mapping alignment file for each of my two ChIP-seq samples. Then, I did heatmap for 400 interested genes of the two mapping files. Now, I was wondering is there a tool that I can use to pick genes that have diferent profiles in the two heatmaps? Thank you very much, Ren ...
chip-seq heatmap differentiate written 4 months ago by lnaren10 • updated 4 months ago by Jennifer Hillman Jackson25k
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Comment: C: multi bam summary
... Hi Jen, The problem was solved after I used the BWA tool to do the mapping. I also sorted the bam file before using mutibamsummary tool. Thank you very much, Ren ...
written 5 months ago by lnaren10
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multi bam summary
... Hello, I was trying to use mutibamsummary tool to generate the read coverage for 8 filtered Bam files(using SAMTOOLS, Filter SAM or BAM, output SAM or BAM ). These 8 filtered Bam files came from the ChIP seq data, which were mapped to the same genome(using Bowtie). But got error saying "No common c ...
chip-seq bam error sort samtools written 5 months ago by lnaren10 • updated 5 months ago by Jennifer Hillman Jackson25k
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Answer: A: Bowtie mapping result
... Thank you very much Jen! Just wondering is there any tutorial for checking the enrichment of methylation on histone by using ChIP-seq? ...
written 5 months ago by lnaren10
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Bowtie mapping result
... Hello, I used "Map with Bowtie for Illumina" tool to map the sequences reads to the reference genome and didn't change any settings (commonly used). Just wondering does the mapping results contain unmapped reads? After the work done, it showed "Map with Bowtie for Illumina on data 59 and data 5: ma ...
chip-seq bam sam bowtie filter written 5 months ago by lnaren10
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trimming illumina single end DNA seq
... Hello, I am trying to trim a single ended  DNAseq by using Trimmomatic tool. But "Input fastQ file" shows that "No fastqsanger dataset available". Same problem happened when I tried to use Map with bwa for Illumina tool as well. I have uploaded the file into history. How can I complete the trimmin ...
galaxy bwa written 2.8 years ago by lnaren10 • updated 2.8 years ago by Jennifer Hillman Jackson25k
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Comment: C: upload file through ftp
... Hi, The browser that i was using was IE(version10). But now, I am able to upload files after I changed the browser to Firefox. Thank you very much for your help! Ren ...
written 2.9 years ago by lnaren10
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Comment: C: upload file through ftp
... Hi Jen, I checked the Preferences, it shows that I am using 0 bytes of disk space. I have not been able to upload anything since I tried using Galaxy. All my job is not initiating at all. I tried to upload a reference fasta file which is 80 Mb from local file, but It won't initiate  the job too. ...
written 2.9 years ago by lnaren10
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upload file through ftp
... Hi, I have been trying to upload a file (29.5G) through ftp. When click "choose FTP file", I can see my file listed in FTP file. I chose the file by adding a check mark in front of the file name, then I clicked "start". But I don't know why it won't upload the file? Thanks   PS: I used FileZilla ...
ftp upload written 2.9 years ago by lnaren10 • updated 2.9 years ago by Nate Coraor3.2k

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