Bowtie why it does not take the 1_sequence.txt nor for bowtie nor the Convert
Dear Sir I try to use Bowtie mapping in galaxy , I import my Illumina s_1_sequence.txt , then I try to use the convert my userName is my email 21: FASTQ Groomer on data 9 An error occurred running this job: /There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have/ but I do have for all the files an error I upload the data using URL http://home.adm.unige.ch/~prnfg/HowardRiezman/wt(RH%20448)%20s_1_sequence.tx... http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-1B%20erg3%209f-10A-1B%20s_1... http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-9D%20erg3%2013f-9D-9D%20s_... http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-13B%20erg3%2013f-9D-13B%20... http://home.adm.unige.ch/~prnfg/HowardRiezman/erg3%20RH%205702%20erg3%20s_1_... http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-3A%20erg3%209f-10A-3A%20s_1... Could you advice me ? Best regards
Hello Olivier, The first place to start is to change the metadata for the history items so that the filetype is .fastq. Do this by clicking on the pencil icon for each dataset, change the filetype, and save. Or, rename the files before transfer. If there are still problems, double check the actual fastq file format first - if the data are large (over 2G) consider using direct FTP to reduce the chance of file corruption during transfer (instructions are on the Upload form). Also please feel free to share a link to your history containing the problem data and we can try to offer advice. (Options -> Share or Publish). You can send the share link back directly to me. Apologies for the delay in reply, Best, Jen Galaxy team On 4/14/11 9:24 AM, Olivier Schaad wrote:
Dear Sir
I try to use Bowtie mapping in galaxy , I import my Illumina s_1_sequence.txt , then I try to use the convert
my userName is my email
21: FASTQ Groomer on data 9 An error occurred running this job: /There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have/
but I do have for all the files an error
I upload the data using URL
http://home.adm.unige.ch/~prnfg/HowardRiezman/wt(RH%20448)%20s_1_sequence.tx... http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-1B%20erg3%209f-10A-1B%20s_1... http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-9D%20erg3%2013f-9D-9D%20s_... http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-13B%20erg3%2013f-9D-13B%20... http://home.adm.unige.ch/~prnfg/HowardRiezman/erg3%20RH%205702%20erg3%20s_1_... http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-3A%20erg3%209f-10A-3A%20s_1...
Could you advice me ?
Best regards
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
participants (2)
-
Jennifer Jackson -
Olivier Schaad