I recently received the data from the sequencing lab. ESTs were sequenced with 454 sequencer and assembled using gsAssembler (v2.6).
This is totally new area for me. Actually, I am not sure if I they gave me all the necessary result files.
Could you tell where from the result files I can find these data:
• number of high quality ESTS
• average length of quality sequence
• number of contigs
• number of singlets
• total number of unique sequences (unigenes?)
• number of ESTs assembled into contigs
• average G+C content of unigenes
• Total raw reads
• Total bases
• Reads after quality control and trimming
• Bases entering assembly
• Aligned reads
• Aligned bases
• Assembled reads
• Repeats
• Outliers
• Too short
• Total isogroups
• Average contig content
• Largest contig content
• Number with one contig
• Average isotig content
• Largest isotig content
• Number with one isotig
• Total isotigs
• Number of bases
• Average isotig size
• Largest isotig size
• Number of contigs
• Average contig size
• Largest contig size
• unassembled reads
• how many read/contigs
• how many % contigs contained 10 read or more
• how many were removed due to their length or because of their low quality score
Thanks a lot!
This is totally new area for me. Actually, I am not sure if I they gave me all the necessary result files.
Could you tell where from the result files I can find these data:
• number of high quality ESTS
• average length of quality sequence
• number of contigs
• number of singlets
• total number of unique sequences (unigenes?)
• number of ESTs assembled into contigs
• average G+C content of unigenes
• Total raw reads
• Total bases
• Reads after quality control and trimming
• Bases entering assembly
• Aligned reads
• Aligned bases
• Assembled reads
• Repeats
• Outliers
• Too short
• Total isogroups
• Average contig content
• Largest contig content
• Number with one contig
• Average isotig content
• Largest isotig content
• Number with one isotig
• Total isotigs
• Number of bases
• Average isotig size
• Largest isotig size
• Number of contigs
• Average contig size
• Largest contig size
• unassembled reads
• how many read/contigs
• how many % contigs contained 10 read or more
• how many were removed due to their length or because of their low quality score
Thanks a lot!
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