Hi, I am in the process of analysing a set of fastq files (paired-end, human). I annotate the reads with information, which is basically a long string of numbers and short sequences, eg:
@HWI-D00595:74:C6DWYANXX:6:1101:1230:2158 *1:N:0:TCCGGAGACGCTCTGA:CUSTOM:1:126:14:9.0:14:100:0:252:42:7:7:42:1.59:ATATGTATACATAT:.:.:126:1.0* ATATGTATACATATATATGTATACATATATATGTATACATATATATGTATACATATATATGTATACATATATATGTATACATATATATGTATACATATATATGTATACATATATATGTATACATAT +HWI-D00595:74:C6DWYANXX:6:1101:1230:2158 1:N:0:TCCGGAGACGCTCTGA /</<<F<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFF/FFFFFFFFFFFFF/BFFFFFFFFFFFFBBFBF<BFFF<B/B/FFF<BBFF# @HWI-D00595:74:C6DWYANXX:6:1101:1149:2167 *1:N:0:TCCGGAGACGCTCTGA:CUSTOM:4:124:16:6.9:18:81:14:123:45:4:4:44:1.47:TATATATCATATATATGA:ATG:AT:126:0.488095238095* ATGTATATACATATATATGAATATATATTCATATATATGTATATACATATATATGTATATACATATATATGAATATATATATATGTATATACATATATATATATGAATATATATTCATATATATAT +HWI-D00595:74:C6DWYANXX:6:1101:1149:2167 1:N:0:TCCGGAGACGCTCTGA BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFBFFFFFFFFFFF/FFFFFF</BFFFFFFFFFF//<BFFFFFFF/<<BBFFFFFF I have highlighted the annotation in bold, part of it is the standard annotation such as read number (1 vs 2) and barcode. Now, when I align this with bwa mem I use the "-C" flag, this prints this flag to the samfile after each alignment, which is great, the problem is that samtools complains about this format: -bash-3.2$ samtools view test_1_annotated.sam [E::sam_parse1] unrecognized type [W::sam_read1] parse error at line 95 [main_samview] truncated file. Removing the annotation makes samtools run without an issue. I know the annotation violates the samtools format according to the docs. So my question is, is there some other way that I can incorporate this annotation and tug it along with my analysis further downstream (such as filtering using samtools etc)? Kind Regards, Piet Jones
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