rsem bam statistics

[ZHONG Huan]

Since I know "rsem-plot-model" could plot the statistics of mapping, like unique mapped reads. However, is there possible that when using the following command, I could get the bam statistics (numbers in text file) like the output from the STAR(*Log.final.out) 

                                                  "rsem-calculate-expression --star \

                           --star-path /sw/STAR \
                           --gzipped-read-file \
                           -p 8 \
                           /data/mmliver_1.fq.gz \
                           /data/mmliver_2.fq.gz \
                           /ref/mouse_125 \ 

                                                           mmliver_paired_end_quals "

Thanks so much

[Bo Li]

Hi Zhong,

You can find the statistics in 'sample_name.stat/sample_name.cnt' file.
The format is as follows:

# '#' marks the start of comments (till the end of the line)
# *.cnt file contains alignment statistics based purely on the alignment
results obtained from aligners
N0 N1 N2 N_tot # N0, number of unalignable reads; N1, number of
alignable reads; N2, number of filtered reads due to too many
alignments; N_tot = N0 + N1 + N2
nUnique nMulti nUncertain # nUnique, number of reads aligned uniquely
to a gene; nMulti, number of reads aligned to multiple genes; nUnique +
nMulti = N1;
# nUncertain, number of reads aligned to
multiple locations in the given reference sequences, which include
isoform-level multi-mapping reads
nHits read_type # nHits, number of total alignments.
# read_type: 0, single-end read, no quality
score; 1, single-end read, with quality score; 2, paired-end read, no
quality score; 3, paired-end read, with quality score

# The next section counts reads by the number of alignments they have.
Each line contains two values separated by a TAB character. The first
value is number of alignments. 'Inf' refers to reads filtered due to too
many alignments. The second value is the number of reads that contain
such many alignments

0 N0
...
number_of_alignments number_of_reads_with_that_many_alignments
...
Inf N2

Hope it helps,
Bo

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[ZHONG Huan]

Hi Bo, thanks a lot, it helps!

Best,

Huan

在 2016年11月3日星期四 UTC+8上午10:06:57，ZHONG Huan写道：