User: mohammedtleis

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Posts by mohammedtleis

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Comment: A: fetch genome all fasta tool not found in tool shed
... Dear Jen, I am still getting internal server error: [Snapshot][1] Best Regards, M. Tleis [1]: https://drive.google.com/file/d/0B6SofYk5XwcMMElUdGtpd09UV0E/view?usp=sharing ...
written 22 days ago by mohammedtleis0
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Comment: A: fetch genome all fasta tool not found in tool shed
... Thanks! I am still issues using the 'fetch_genome_dbkeys_all_fasta'. After installing , I click on 'Manage Installed Tools' and Click on the button to create a new DBKey or reference genome, But Galaxy got an internal error and a message is supposedly sent to Galaxy team. Now what? Best Regards, ...
written 29 days ago by mohammedtleis0
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fetch genome all fasta tool not found in tool shed
... Greetings, I am looking for the fetch-genome-all-fasta tool to install it on local instance of galaxy; I want to use it to fetch a human genome to be used as a reference genome. But I couldn't happen to find this tool when I search in the toolshed. I could find it online though and cloned it into ...
fetch index dbkey genome data-manager written 4 weeks ago by mohammedtleis0
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Comment: C: Building a human reference genome
... Thanks Jennifer! I downloaded the hg38.fa.gz, but I couldn't upload it to galaxy since it is larger than 2 GB and It asked to do so via ftp? So far, I found this link: [Install some ftp server][1]. I did install and configured proftpd. But I am not sure how to connect it to Galaxy's database. Is th ...
written 5 weeks ago by mohammedtleis0
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Building a human reference genome
... Dear Biostars, I would like to build the index for human genome to be used as a reference genome in a local instance of Galaxy. The starting point is to obtain the genome files from UCSC through 'ftp' to 'hgdownload.cse.ucsc.edu'. If I navigate to the ./hg38/bigZips , I would find many different f ...
galaxy written 6 weeks ago by mohammedtleis0 • updated 6 weeks ago by Jennifer Hillman Jackson23k
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Does re-sequencing fastq files contain DNA or RNA sequences?
... Dear Biostar members, I have a very basic question about some fastq files I got. All what I know is that they are re-sequencing fastq files. My question is whether they are actually DNA or RNA sequences? In general, Is there a way to tell by looking into the contents? Does it matter to know this? ...
galaxy rna-seq written 7 weeks ago by mohammedtleis0 • updated 7 weeks ago by Jennifer Hillman Jackson23k
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TopHat Error stating that (installed) Bowtie2 is not installed
... I tried to try 'TopHat (v.2.1.0)' locally to align some RNA-Seq data to a reference human genome. The tools execution has failed stating that bowtie 2 is not found. However, Bowtie2 (v.2.3.0.1) is installed and I can verify it in my local tool shed (revision 937aa69e715f). Here is the error after ...
rna-seq galaxy bowtie software error alignment written 6 months ago by mohammedtleis0
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Getting an error when trying to align sequence data with bowtie2
... On a local instance of galaxy, I created a reference gnome and tried to use 'bowtie2' to align some sequence data with the reference gnome. After waiting for hours, I got the following error: Traceback (most recent call last): File "/Users/tleis/GitHub/galaxy/galaxy/lib/galaxy/jobs/runners/l ...
chip-seq galaxy alignment written 6 months ago by mohammedtleis0 • updated 6 months ago by Jennifer Hillman Jackson23k
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Comment: C: How to create a Fasta file of mouse genome from download chromosome files
... Thank you Devon for your answer, I find it so helpful. Now I have three questions/issues: 1. Does it matter in what order the files are combined? Would bowtie2 be able to automatically locate the corresponding information throughout the file? In case the order is important where should be the unkno ...
written 6 months ago by mohammedtleis0
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How to create a Fasta file of mouse genome from download chromosome files
... Dear Biostar members, My intention is to create a genome reference of the mouse (mm10) to be used within bowtie2. So far, I downloaded the fa files and have the files listed below after my question. Now I need to combine the files into one fa file to be used as reference genome for bowtie2. My qu ...
chip-seq galaxy written 6 months ago by mohammedtleis0 • updated 6 months ago by Devon Ryan1.7k

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