I have a set of merged unpaired reads (RNA seq data) that are in ASCII text format (e.g. sample1_MERGED). I've used Megahit to co-assemble them and get the contig files. Now I wish to get the BAM files using Bowtie but I am not sure how it is done properly for unpaired reads like those I have. The unpaired reads are as below:
>demoneme_02_60847700|K00242:68:H7FKMBBXX:5:2201:28534:49247 1:N:0:GGCTAC|o:36|m/o:0.000000|MR:n=0;r1=0;r2=0|Q30:n/a|CO:0|mismatches:0 atggacgatatcttttacaaaaaaagtgtcttgcgtagaaatacaacttccggtgagaacaagacttgacaaaactccaaaattatttgtcgcttttttgactccctgaatttgaatagtaagatacccaattgggatattggtccattctcccacataaaatt >demoneme_02_60847705|K00242:68:H7FKMBBXX:5:2201:31050:49247 1:N:0:GGCTAC|o:75|m/o:0.000000|MR:n=0;r1=0;r2=0|Q30:n/a|CO:0|mismatches:0 agaaggtagggatgacgtcaagtcatcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcgacctcgcgagagcaagcggacctcataaagtgcgtcgtagt
Based on the manual, I tried to use the flag -U <my files=""> as the following:
bowtie2 -x 2 ../04_MAPPING/contigs -U sample1_MERGED --no-unal -S ../04_MAPPING/sample1.sam
Then I get this error: Error: reads file does not look like a FASTQ file
Which tells me that my files are not in fastq format.
And if I use --tab5 instead of -U as below:
bowtie2 --threads 2 -x ../04_MAPPING/contigs --tab5 sample1_MERGED --no-unal -S ../04_MAPPING/sample1.sam
Then I won't get an error but below message:
0 reads 0.00% overall alignment rate
Does Bowtie support single merged (unpaird) reads in txt formats as an input? Any help/advice would be much appreciated. Please let me know if my question is not clear enough.