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Question: problems with Tophat2
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gravatar for dawn.oreilly
4.4 years ago by
dawn.oreilly • 10
United Kingdom
dawn.oreilly • 10 wrote:

HI there,

I am attempting to use Tophat2 (version 0.6) but when I select paired-end reads I don't get a window to add the other paired FASTA file. Can you help please?

thanks

Dawn
rna-seq • 897 views
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by dawn.oreilly • 10

Hi Dawn,

What server are you using? Galaxy Main at http://usegalaxy.org? Or another public site (please share which), local, or cloud?

Thanks, Jen, Galaxy team

ADD REPLY • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k

I am using the usegalaxy.org<http: usegalaxy.org=""> Dawn

Dawn O'Reilly James Martin Stem Cell Fellow Sir William Dunn School of Pathology Oxford OX1 3RE

On 20 Jun 2014, at 16:15, "Jennifer Hillman Jackson on Galaxy Biostar" <notifications@biostars.org<mailto:notifications@biostars.org>> wrote:

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Comment: problems with Tophat2 <http: biostar.usegalaxy.org="" p="" 8096="" #8098=""> :

Hi Dawn,

What server are you using? Galaxy Main at http://usegalaxy.org? Or another public site (please share which), local, or cloud?

Thanks, Jen, Galaxy team

ADD REPLY • link written 4.4 years ago by dawn.oreilly • 10
0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Dawn,

When the tool form option "Is this library mate-paired?: Paired-end" is select, the form resets to permit the selection of two .fastqsanger datasets "RNA-Seq FASTQ file, forward reads:" and "RNA-Seq FASTQ file, reverse reads:"

These three options are the first listed on the tool form. Please double check the FASTQ input datasets and adjust the datatype/quality scaling as needed. Help is here:
https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Hopefully you have discovered this, but if not, this helps! Jen, Galaxy team
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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