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Old 08-05-2014, 08:54 PM   #12
Location: urumqi

Join Date: Jul 2014
Posts: 58
Default fastq to sam

i have a raw reads dataset in format fastq, and i want to use it to find SNPs of the transcriptome data we have. after i searched some material i found that i can do it by using Samtools and SOAPsnp softwares, am i right? but before i use them i need to convert my raw reads fastq format to SAM format, right?
so i installed java, samtools and picard tools on my ubuntu 12.04(why i mention these here is because i am new at linux, so any suggestion would be appreciated). and then i write this commend in the terminal :
java -Xmx2g -jar FastqToSam.jar FASTQ=CD_ATGTCA_L007_R1_001.fastq.gz FASTQ2=CD_ATGTCA_L007_R2_001.fastq.gz OUTPUT=outputfile.sam PREDICTED_INSERT_SIZE=null QUALITY_FORMAT=Solexa SAMPLE_NAME=file4

then i got this :
Error: Unable to access jarfile FastqToSam.jar

i do not know what is going on.
i guess many people here may done these before ,so please anyone could share your knowledge ?!
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