unable to input file in trimmomatic

2.1 years ago by

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.1 years ago by khh • 0

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 REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.1 years ago by khh • 0