User: David K Crossman

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Posts by David K Crossman

<prev • 13 results • page 1 of 2 • next >
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Ngs: Indel Analysis Tool Order
... Hello! I have a question about the NGS: Indel Analysis toolset in Galaxy. I have aligned my samples from Illumina's HiSeq2000 to the reference genome using BWA. I've called SNPs using SAMTools and now need to call indels. Under the NGS: Indel Analysis toolset, I see two options: ...
bam samtools alignment bwa written 6.3 years ago by David K Crossman130 • updated 6.3 years ago by Jennifer Hillman Jackson23k
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Comment: C: Cuffdiff Question About Using An Unspecified (?) Database/Build
... Jen, Thank you very much for the reply. I'm glad to know it is a known bug and not something on my side of things. So, would my analysis be affected if I did change the bam file "Database/Build" to the older tree shrew version found in the drop down list? What significance does this "Dat ...
written 6.3 years ago by David K Crossman130
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Cuffdiff Question About Using An Unspecified (?) Database/Build
... Hello! I have an RNA-Seq project which consists of 5 samples from the species tree shrew. When uploading these fastq files into Galaxy, I chose "unspecified (?)" for the database/build since the latest tree shrew version is not in the drop down list. When using TopHat, Cufflinks/C ...
cufflinks rna-seq written 6.3 years ago by David K Crossman130 • updated 6.3 years ago by Jennifer Hillman Jackson23k
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Cufflinks Reporting Fpkm Values Of All Zeroes (0)
... Hello! I have come across a problem where Cufflinks is reporting all FPKM values as zeroes (0). I have a unique RNA-Seq project from a collaborator where they are studying eyesight by using tree shrews. I found that Ensembl (http://useast.ensembl.org/Tupaia_belangeri/Info/Index) ha ...
cufflinks rna-seq written 6.4 years ago by David K Crossman130 • updated 6.4 years ago by Jennifer Hillman Jackson23k
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Answer: A: Using Files Produced By "Barcode Splitter"
... Jeremy, The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. David To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] using files produced by "Barcode Splitter" I used t ...
written 6.4 years ago by David K Crossman130
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Analyzing Rna-Seq Replicates Using Cuff(Links/Compare/Diff)
... Hello! I have 10 human RNA-Seq samples consisting of 3 groups (2 replicates per group). I have already run each of them through TopHat and Cufflinks on the Penn State Galaxy instance. I am now at a head-scratching moment. I want to use CuffCompare next (in the end I will want to ...
cufflinks rna-seq written 6.4 years ago by David K Crossman130
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Galaxy Server Issues?
... Hello! We uploaded 12 samples to Galaxy last night via FTP. This morning, I went to "Get Data" and clicked on all 12 that were under the FTP location, chose the type of file they were and reference genome and then clicked "Excecute." The 12 moved over to the History panel and after ...
galaxy written 6.5 years ago by David K Crossman130 • updated 6.5 years ago by Nate Coraor3.1k
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Comment: C: Mycoplasma Pneumoniae M129 And Fh Reference Genome
... Jen, Thanks for the useful tips! Yes, the NCBI bioproject link is the correct source for the FH strain. Thanks, David To: David K Crossman Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Mycoplasma pneumoniae M129 and FH reference genome Hello David, The genome for Mycopla ...
written 6.5 years ago by David K Crossman130
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Mycoplasma Pneumoniae M129 And Fh Reference Genome
... Hello! I noticed that Mycoplasma pneumonia M129 and FH are not found in the reference genome in Galaxy. Would it be possible to have both of those in there? Thanks, David ...
galaxy written 6.6 years ago by David K Crossman130 • updated 6.5 years ago by Jennifer Hillman Jackson23k
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Comment: C: Re: Rna Seq Analysis And Gtf Files
... Jeremy, I just wanted to give you an update. Adding the "gene_name" attribute with the gene name into column 9 worked extremely well for Cuffdiff. The columns I referenced below as being blank now have their respective gene name in them! Thank you very much for all your help! Th ...
written 6.7 years ago by David K Crossman130

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