Question: unable to input file in trimmomatic
0
gravatar for khh
13 months ago by
khh0
khh0 wrote:

Preparing for trinity analysis I try to trim questionable 5' bases. Trying to use 'Trimmomatic', I can't load my data set that was analyzed with fastqc. My files show up/ are accessible in other routines.

ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson23k • written 13 months ago by khh0
0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

These are fastq datasets? They might be too large to load with the "Browse for local file" option. Try FTP instead. This is how: https://wiki.galaxyproject.org/Support#Loading_data

Thanks, Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson23k

Hi Jennifer,

Thanks for the response. I do have my data files (uploaded as you suggested with FTP). They do show up in some routines but not in the ones I need.

KHH

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Wednesday, November 02, 2016 2:34 PM To: khh@louisiana.edu Subject: [BULK] [galaxy-biostar] unable to input file in trimmomatic Importance: Low

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 Answer: unable to input file in trimmomatic http://biostar.usegalaxy.org/p/20384/#20386 :

Hello,

These are fastq datasets? They might be too large to load with the "Browse for local file" option. Try FTP instead. This is how: https://wiki.galaxyproject.org/Support#Loading_data

Thanks, Jen, Galaxy team


You may reply via email or visit http://biostar.usegalaxy.org/p/20384/#20386

ADD REPLYlink written 13 months ago by khh0
1

By routines do you mean tool forms? If so, the problem could be the datatype assignment. Some tools will require just fastq and others will require fastqsanger.

https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson23k

Thank you - it was the wrong data format. Unfortunately the required FASTQ Groomer is under ‘NGS: QC and manipulation’ not under ‘Convert Formats’.

KHH

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Wednesday, November 02, 2016 3:59 PM To: khh@louisiana.edu Subject: [galaxy-biostar] unable to input file in trimmomatic

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: unable to input file in trimmomatic http://biostar.usegalaxy.org/p/20384/#20389 :

By routines do you mean tool forms? If so, the problem could be the datatype assignment. Some tools will require just fastq and others will require fastqsanger.

https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA


You may reply via email or visit http://biostar.usegalaxy.org/p/20384/#20389

ADD REPLYlink written 13 months ago by khh0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 107 users visited in the last hour