I have a question that is quite similar to questions that were already asked. However, reading those threads, I could not solve my problem:
I want to assemble Illumina short paired end reads. I actually have data from two lanes. I managed to convert the numeric SCARF files to fastq files. I checked whether the paired reads are in the same order for the two files for each of the lanes. I also checked if there are very short reads. Both (non-pairing and short reads) were reported to cause segfaults.
When I analyse the data from the first lane, I can successfully finish the maq map command. However, for the data from the second lane, maq map stops and I get a segfault.
I tried different version of MAQ and even tried pre-compiled versions.
The command I use is analogue to:
maq map out.aln.map s_5_1.fastq s_5_2.fastq
I would be very happy, if somebody can help me out!
Thanks and best regards
Molecular Microbiology and Biotechnology
Institute of Biology Leiden
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