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Obtains statistics from the reads quality of a fastq file. The binary output is then read by an Rmd
script that generates a html visualization of the data.
Usage C
executable (in folder bin
):
int
(4B) : read length (read_len
),int
(4B) : number of tiles (ntiles
),int
(4B) : minimum quality accepted (minQ
), int
(4B) : number of possible qualities (nQ
),int
(4B) : number of reads (nreads
),int
(4B) : number of reads containing N's (reads_wN
),int
(4B) : size of lowQ_ACGT_tile
, see below (sz_lowQ_ACGT_tile
),int
(4B) : size of ACGT_tile
, see below (sz_ACGT_tile
),int
(4B) : size of reads_MlowQ
, see below (sz_reads_MlowQ
),int
(4B) : size of QPosTile_table
, see below (sz_QPosTile_table
),int
(4B) : size of ACGT_pos
, see below (sz_ACGT_pos
),ntiles*int
(4xntiles
B) : tile tags (tile_tags
),ntiles*int
(4xntiles
B) : lane tags (lane_tags
),nQxint
(4xnQ
B) : quality tags (quality tags
),5 x ntiles x (long int)
(5xntiles
x8B) : # (A,C,G,T,N) per tile with low quality (lowQ_ACGT_tile
),5 x ntiles x (long int)
(5xntiles
x8B) : # (A,C,G,T,N) per tile (ACGT_tile
),(read_len+1) x (long int)
((read_len
+1)x8B) : # reads with at least m
low quality base callings (reads_MlowQ
),ntiles x read_len x nQ x (long int)
(ntiles
xread_len
xnQ
x8B) : base callings per tile per position with a given quality (QposTile_table
).5 x read_len x (long int)
(5xread_len
x8B ): # (A,C,G,T,N) per position, (ACGT_pos
)NOTE If the data were sequenced on more than one lane, in Plots 3, 4 and 5 there will be a heatmap pro lane.
An example is given in the folder examples/QReport_Sreport
. To run an example, type,
and compare it with the provided run example, as specified in the README file under ./example/QReport_Sreport
Paula Pérez Rubio
GPL v3 (see LICENSE.txt)