Re: [galaxy-user] Help!! Tophat paired end reads
Hi Jennifer, This is a subject I'm interested in. I wonder if you could share a workflow to estimate percentage of reads mapping to for example exomes(I can get the coordinates for a GFF dataset). I have a mapping result for RNA-seq data and by looking in the browser, it seems to also have a lot of reads mapping outside of exomes, but I would like to put numbers on it. Thanks, Carlos P.D. I'm trying now to get GATK's 'Depth of Coverage' to work, but I'm having some issues with it. Is there any other options in Galaxy? On Mon, Apr 16, 2012 at 12:27 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Jiwen, The bioinformatics part of your analysis sounds as if it went fine, so that is good news. This list may not be the best place to get feedback about library construction methods, but we can see who has help to offer. I did a quick search myself and found this recent publication that includes a comparison of rRNA depletion methods with mapping profiles: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027288 Best, Jen Galaxy team On 4/15/12 8:24 AM, 杨继文 wrote: Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons or span exons (splice junction). These reads seem to fit very well. However, I can also see a lot reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping was wrong? Did anybody have similar experience?? Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than the coding region). Is this normal? Is this caused by the rRNA depletion method ? Looking forward to your reply Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Help!! Tophat paired end reads
Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons or span exons (splice junction). These reads seem to fit very well. However, I can also see a lot reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping was wrong? Did anybody have similar experience?? Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than the coding region). Is this normal? Is this caused by the rRNA depletion method ? Looking forward to your reply Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Help!! Tophat paired end reads
Hi Jiwen, The bioinformatics part of your analysis sounds as if it went fine, so that is good news. This list may not be the best place to get feedback about library construction methods, but we can see who has help to offer. I did a quick search myself and found this recent publication that includes a comparison of rRNA depletion methods with mapping profiles: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027288 Best, Jen Galaxy team On 4/15/12 8:24 AM, 杨继文 wrote: Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons or span exons (splice junction). These reads seem to fit very well. However, I can also see a lot reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping was wrong? Did anybody have similar experience?? Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than the coding region). Is this normal? Is this caused by the rRNA depletion method ? Looking forward to your reply Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
