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Old 01-13-2010, 01:05 PM   #1
etk1220
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Default Bfast Sam format

Hello,

I am trying to map solid reads to a reference file using bfast, and during the post-processing step, when I try to get the output in sam format, bfast begins processing the reads and immediately prints the error message:
AlignedReadConvert.c:705: AlignedReadConvertPrintAlignedEntryToSAM: Assertion `strlen(qual) == strlen(read)' failed.
Abort

I checked the length of the qual line in the fastq file that I used and it was equal to the length of the sequence line. I also tried post processing with the output in baf format, and then converting to .sam format using bafconvert, but that resulted in the same error during the conversion step.

Any help in this matter would be greatly appreciated.

Thanks,
etk1220
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Old 01-13-2010, 01:14 PM   #2
nilshomer
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Default

Quote:
Originally Posted by etk1220 View Post
Hello,

I am trying to map solid reads to a reference file using bfast, and during the post-processing step, when I try to get the output in sam format, bfast begins processing the reads and immediately prints the error message:
AlignedReadConvert.c:705: AlignedReadConvertPrintAlignedEntryToSAM: Assertion `strlen(qual) == strlen(read)' failed.
Abort

I checked the length of the qual line in the fastq file that I used and it was equal to the length of the sequence line. I also tried post processing with the output in baf format, and then converting to .sam format using bafconvert, but that resulted in the same error during the conversion step.

Any help in this matter would be greatly appreciated.

Thanks,
etk1220
If you are aligning SOLiD reads the quality string should be one character fewer than the sequence string. i.e.

OK:
Code:
>READ
T00000
+
IIIII
NOT OK:
Code:
>READ
T00000
+
IIIIII
If you are not aligning SOLiD reads then can you check that there are no whitespaces in your sequence or quality strings?
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Old 02-02-2010, 11:43 AM   #3
niazi84@hotmail.com
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Default How to view output

Hello,

I am new to BFast. I have executed the sample data from tutorial's commands. Now i have .sam reported file. Can anybody tell me how to view this file. Will i have to use other software to view the result? Thanks
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Old 02-02-2010, 06:25 PM   #4
nilshomer
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Quote:
Originally Posted by niazi84@hotmail.com View Post
Hello,

I am new to BFast. I have executed the sample data from tutorial's commands. Now i have .sam reported file. Can anybody tell me how to view this file. Will i have to use other software to view the result? Thanks
The SAM format is described here and can be manipulated by SAMTools or Picard. Genome viewers (like IGV) can view the alignments. Feel free to search past posts or the software hub here at seqanswers for many interesting and helpful posts on each of these types of software.
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