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Old 08-05-2014, 11:40 PM   #14
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Join Date: Apr 2012
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Originally Posted by kurban910 View Post
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 ?!
SAM is the abbreviation for Sequence Alignment/Map format, which tells you that it should contain aligned/mapped reads. Though it is possible to create a kind of unmapped SAM file from fastq, this will be useless to address your question.

My suggestion: Make yourself familiar with read alignment via tophat (the software is here:; the paper is here: and samtools in general (I suggest Dave Tang's brief wiki: and samtools mpileup in particular (
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