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Old 06-01-2010, 11:22 AM   #1
albrown415
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Default FASTQ to SAM conversion

What is the best program to use for converting fastq (or eland extended) files to SAM format? Thanks!
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Old 06-01-2010, 11:46 AM   #2
nilshomer
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Quote:
Originally Posted by albrown415 View Post
What is the best program to use for converting fastq (or eland extended) files to SAM format? Thanks!
Do you want to align the data first, or just represent the FASTQ data in the SAM format? Is the data paired end (mate-pair)?
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Old 06-02-2010, 08:20 AM   #3
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You're right. This was a silly question. Most people map the reads at this point and choose an alignment program that outputs the data into the proper format. I'm working to get Bowtie running on my computer, which I believe should be able to input fastq and output SAM.
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Old 06-04-2010, 12:28 PM   #4
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If you did want to convert the FASTQ to an unaligned SAM or BAM file, try this:
http://picard.sourceforge.net/comman...tml#FastqToSam
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Old 06-04-2010, 01:59 PM   #5
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Thanks. That's great to know.
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Old 01-04-2012, 07:03 AM   #6
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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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Old 01-04-2012, 11:55 AM   #7
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Originally Posted by ebatis2 View Post
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!!
FASTQ 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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Old 12-10-2012, 10:00 PM   #8
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Originally Posted by husamia View Post
FASTQ 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.
I have the raw FASTQ reads and in order to perform de novo assembly using transAbySS, I need to feed the input in the form of bam or sam. Can you please shed some light on this.
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Old 12-11-2012, 05:23 PM   #9
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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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Old 12-13-2012, 11:57 PM   #10
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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,
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Old 01-24-2013, 01:57 AM   #11
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Thanks TheRob and Stroehli !!

TheRob - I was using transbyss for de-novo assembly, since I don't have a concrete reference to begin with.

Stroehli - I have used abyss to assemble the contigs. thank you.
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Old 08-05-2014, 08:54 PM   #12
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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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Old 08-05-2014, 09:02 PM   #13
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To access the jar, you can try giving complete path of the jar where it is installed. That should work.
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Old 08-05-2014, 11:40 PM   #14
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Quote:
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: 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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Old 08-06-2014, 12:34 AM   #15
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Since you mention SNP calling, you'll want to use a tools like BWA or bowtie2 rather than tophat for alignment. Aside from that, I'm in agreement with WhatsOEver.
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Old 08-06-2014, 12:51 AM   #16
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Quote:
Originally Posted by dpryan View Post
Since you mention SNP calling, you'll want to use a tools like BWA or bowtie2 rather than tophat for alignment. Aside from that, I'm in agreement with WhatsOEver.
Agreed
I mentioned tophat as it has imo the best documentation and is therefore the easiest to start with. But in the end, it might not be the best solution here.
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Old 08-06-2014, 02:36 AM   #17
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i am glad for you guys reply, thanks.

Last edited by kurban910; 08-06-2014 at 03:00 AM.
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Old 08-06-2014, 08:25 AM   #18
kurban910
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hello guys!
i have downloaded bwa-0.7.10, and then uncompressed it, then
kurban@kurban-X550VC:~/Downloads/bwa-0.7.10$ make

it showed this :
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
utils.c:33:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [utils.o] Error 1
what is what is happening there ?
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Old 08-06-2014, 08:30 AM   #19
maubp
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You (or your SysAdmin) need to install the zlib library including the development files (header files like zlib.h).
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Old 08-06-2014, 09:03 AM   #20
kurban910
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thank you, after installing zlib it worked
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