What is the best program to use for converting fastq (or eland extended) files to SAM format? Thanks!
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If you did want to convert the FASTQ to an unaligned SAM or BAM file, try this:
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Hi,
I've received results from my first NGS run and like you posted, I'd like to convert my fastq file to a SAM file in order to upload and retrieve data from Galaxy. I'll need to map the reads and align them to the Rice genome...but is this something I could do on my MacOSX? I'm at a loss as far as how to retrieve the sequencing results! Any help would be greatly appreciated!!
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Originally posted by ebatis2 View PostHi,
I've received results from my first NGS run and like you posted, I'd like to convert my fastq file to a SAM file in order to upload and retrieve data from Galaxy. I'll need to map the reads and align them to the Rice genome...but is this something I could do on my MacOSX? I'm at a loss as far as how to retrieve the sequencing results! Any help would be greatly appreciated!!
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Originally posted by husamia View PostFASTQ is the raw reads with qualities. SAM is format to describe reads and their alignment. This was hinted in the previous respond above. It seems you've got to align the reads first if you just received the raw FASTQ. Perhaps you should be asking how to align your reads. I can't help much because I am not sure what your goal is. Galaxy has a tutorial on how to align your reads and produce a SAM file. Check it out.
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Hi Amolkote,
It is rather unusual for an assembly program to accept SAM/BAM input but not FastQ. I suspect it accepts FastQ, but I don't have any experience with transAbyss. Anyways, the only tool i know that will do the job (short of an awk or perl script, which can be dangerous) was mentioned above by maubp: FastqToSam.
Why are you using transAbyss exactly?
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Hi,
I think you cannot run transAbyss on its own. Taking a short look at the manual, (http://www.bcgsc.ca/downloads/trans-...v1.2.0.doc.pdf) I figured you probably need to run Abyss first (see "Data Preparation" in the Workflow on page 7). Plus you might have to install all the external software mentioned in "Installation, 2. External Software" (page 5). Abyss will produce contigs (.fa) and the other aligners will produce the SAM/BAM files for you, so you don't have to convert them, if I got that right. Hope it helps.
Cheers,
StroehliMSc Bioinformatics student at the Free University Berlin , Germany
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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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Originally posted by kurban910 View Posti 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 ?!
My suggestion: Make yourself familiar with read alignment via tophat (the software is here: http://ccb.jhu.edu/software/tophat/tutorial.shtml; the paper is here: http://www.nature.com/nprot/journal/....2012.016.html) and samtools in general (I suggest Dave Tang's brief wiki: http://davetang.org/wiki/tiki-index.php?page=SAMTools) and samtools mpileup in particular (http://samtools.sourceforge.net/mpileup.shtml)
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