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Question: Help!! Tophat Paired End Reads
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gravatar for 杨继文
6.6 years ago by
杨继文 • 210
杨继文 • 210 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
rna-seq tophat • 1.2k views
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modified 6.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.6 years ago by 杨继文 • 210
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gravatar for Jennifer Hillman Jackson
6.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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.002 7288 Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k
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?
ADD REPLY • link written 6.6 years ago by Carlos Borroto • 390
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