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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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Originally posted by etk1220 View PostHello,
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
OK:
Code:>READ T00000 + IIIII
Code:>READ T00000 + IIIIII
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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,
etk1220Tags: None
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