Hi all,

I've been given a set of 454 sequences/results and I'm very new with this kind of data.

• 1.XXX.454Reads.fna (i guess these are the fasta sequences for the reads... )
• 1.XX.454Reads.qual (... and the qualities....)
• a tgz file containing some binary *.clc files (?)

• 454AllStructVars.txt.gz 454HCStructVars.txt.gz 454AllDiffs.txt.gz 454HCDiffs.txt.gz : it should be the allele calling. I guess those files were generated by the 'Genome Sequencer FLX System' isn't it ? If not, what is that tool ? I understand the *Diffs files however, the content of *StructVars.txt is not clear to me, for example, how should I interpret the following output:

  >chr19    1988212    <--        ?    ?    ?        2    100.00    -    Point
  Reads with Difference:
  chr19                   1988172+ TTGTATTTTTGGTAGAGGCGGGATTTCATCATGTTGGCCAGACCTCGAGTGATC--CACCTGCCT-TGGCCTCCCAAAGT 1988248
                                                                   *
  GKF3EFN01B3QKI              237-                                         GACCTCG--TGATCTGC-CC-GCCTCTG-CCTCCCAAAGT 203
  GKF3EFN01CM6BB              183+                                         GACCTCG--TGATCTGC-CC-GCCTCTG-CCTCCCAAAGT 217
                                                                   *
  Other Reads:
  

does that mean that only the tail of two reads was mapped on the reference (=deletion) ? what is the <kbd>'*'</kbd> under the reference ?

• is there a way to transform those data to SAM/BAM ?
• how can i get the coverage of the genome with those data ?

Many thanks,

Pierre