Thanks for all the help - I think the clean-up process I am using is what's ruining my pairs... It a specific protocol that has a collapse for identical reads, and I think this is how pairs get lost (i.e. if I have 10 reads identical in each fastq file, the ones which survive are not the original pairs) If I were to align each read separately and than put them into a single file, will I be loosing too much info? each read is 100bp. (btw the reference genome is correct (I double checked).)
Thanks!
No worries.
check this out: Error while running BWA mem
This is not an error, it's an information. Convert created SAM file to BAM file, sort it with samtools and check alignments statistics by samtools flagstat. You will see then how many reads were aligned etc. Best, Agata
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It's possible that your read pairing is broken, or that you're using the wrong reference so nothing is aligning, or the quality is too low for anything to align. Lots of possibilities - I suggest you start by stating what organism you are working with and BLASTing or Sketching the reads to see what they are, and running FastQC and posting the results. Also, the first 10 read headers from each file would be helpful, as well as any information you have about what platform they came from and how they have been preprocessed.