RSEM.stat

[Alicia R. Pérez-Porro]

Hi,

I just got my first RSEM results and i'm trying to understand the output. Can someone tell me what exactly is inside RSEM.stat? I have 3 files: RSEM.cnt, RSEM.model and RSEM.theta and i have no idea what are they.

Thanks,

Alicia

---

Alicia R. Pérez-Porro

PhD candidate

Giribet lab

Department of Organismic and Evolutionary Biology

MCZ labs

Harvard University

26 Oxford St, Cambridge MA 02138

phone: +1 617-496-5308

fax: +1 617-495-5667

www.oeb.harvard.edu/faculty/giribet/

[b...@cs.wisc.edu]

Hi Alicia,

RSEM.cnt stores alignment statistics. RSEM.model is the model of RNA
sequencing process learned from the data. RSEM.theta is the estimated read
generating probability, which can be converted into TPM/FPKM.

These are internal outputs, which are used for simulation/generating
plots. They are designed as black box for users.

Best,
Bo

> Hi,
>
> I just got my first RSEM results and i'm trying to understand the output.
> Can someone tell me what exactly is inside RSEM.stat? I have 3 files:
> RSEM.cnt, RSEM.model and RSEM.theta and i have no idea what are they.
>
> Thanks,
> Alicia
>
>
> ---

> Alicia R. P�rez-Porro

> PhD candidate
>
> Giribet lab
> Department of Organismic and Evolutionary Biology
> MCZ labs
> Harvard University
> 26 Oxford St, Cambridge MA 02138
> phone: +1 617-496-5308
> fax: +1 617-495-5667
> www.oeb.harvard.edu/faculty/giribet/
>

> --
> RSEM website: http://deweylab.biostat.wisc.edu/rsem/
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>

[Oleg Moskvin]

Hi Bo,

Would you please shine some light into one of those "black boxes"?
In particular, I believe the alignment statistics (*.cnt files under *.STAT folder) may be useful for the end user.
I see 17 (undocumented) lines there.
Would it be possible to annotate them?

Thanks!

Oleg

[Bo Li]

Hi Oleg,

Sorry to reply you late.

Sure thing. Please see below for an annotation of the *.cnt file. I'll
include it in next RSEM release.

Best,
Bo


# '#' 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

>>> www.oeb.harvard.edu/faculty/giribet/ [1]
>>>
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>>> RSEM website: http://deweylab.biostat.wisc.edu/rsem/ [2]

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>
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[celine noirot]

Hi,
So why nUnique is not equal to the line number of alignment 1 ?

It's seems that number of unique read alignement is nUnique - nUncertain.
Could you confirm it ?
Best
Céline