Question: splitter not working
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souradeep.mis • 40 wrote:
hi everybody. i am very inexperienced in this area, so if you guys can kindly help me to solve my problem it will be very greatful of you guys. for the past three days i am trying fastq splitter to split my illumina paired end single dataset into two by uploading them into galaxy. but each time it failed. this time i uploaded only one SRA files which ran for more than 24 hours but the files did not split. my file is of about 7.5 gb in size and in fastqsanger format. what should i do now, is there any other way around?
please help me, otherwise my work is stuck.
thanks a lot.
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modified 2.0 years ago
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Jennifer Hillman Jackson ♦ 25k
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2.0 years ago by
souradeep.mis • 40
I'm slightly confused by your question :) Do you have problems uploading your huge datafile, or is it already in Galaxy and you have problems with the tool "fastq splitter"? Moreover, do you have a FASTQ file or an SRA archive?
thank you for your kind reply Sir. no my file is already in galaxy, but when i am giving my fastq files in FASTQSplitter , the splitter keep on rotating and ultimately gets terminated, and the error comes as "the program has run too long than expected". and my files are fastq files. so i think my problem is with the tool.
Yes, seems so! What do you want to do?
Yes, seems so! What do you want to do?
i want to assemble these files using trinity, if i give all my data as paired end , then trinity requires each end data separately, which i cant give without spitting. if i am wrong please correct me, and if there are any other options i can follow then please mention them so that i can get some alternative. even i have tried to split these fastq files with fastq-dump so that '/1' and '/2' gets separated, but the command is not working and showing error. thank you sir, your reply gives me hope.