Unidentified Reads in Base Calls

[dlhmmll]

When looking for my .fasta files under MiSeq Analysis > Data > Base Calls, there are always small .fasta files called "unidentified". Why do I get these, what are they, and are they useful? I'm doing meta-transcriptomic sequencing and I care more for the presence of the RNA virus than the host. The "unidentified" sequences tend to be from pathogen.

Thanks

[dlhmmll]

Correction: I mean "undetermined"

Correction: I mean "undetermined". I usually don't spike my runs with PhiX either

[GenoMax]

If you are referring to sequences in "undetermined" files then these reads contain indexes that don't fit expected results (based on the samplesheet that you provide that has SampleID_Index mapping). There can be tens of variations of index sequences in there. Some of those are sequencing/basecalling errors. These reads are not generally useful (unless there was an error in the samplesheet and real samples end up in this pool). This pool will also contain phiX reads (since it does not have an index).

[shreedivya]

FASTA format is the text-based format for representing the nucleotide sequences and the peptide sequences. In this the base pairs or amino acids are represented by using single-letter codes. A sequence in FASTA format begins on a single-line description, followed by the lines of sequence data.

[dlhmmll]

Thanks for the replies

[shreedivya]

Nice post.