Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in / Register
Toggle navigation
Menu
Open sidebar
Holly Ruess
celseq2
Commits
1839866a
Unverified
Commit
1839866a
authored
Apr 16, 2018
by
Yun YAN
Committed by
GitHub
Apr 16, 2018
Browse files
🇨🇳
release v0.5.2
v0.5.2-b
parents
81fad008
b044f324
Changes
4
Hide whitespace changes
Inline
Side-by-side
celseq2/qc.py
View file @
1839866a
...
...
@@ -84,12 +84,12 @@ def plotly_qc(fpath, saveto, sep=',', name=''):
total_num_UMIs
=
expr
.
sum
(
axis
=
0
)
num_detected_genes
=
(
expr
>
0
).
sum
(
axis
=
0
)
mt_index
=
pd
.
Series
(
[
x
for
x
in
expr
.
index
if
x
.
startswith
(
'mt-'
)
or
x
.
startswith
(
'MT-'
)]
)
mt_index
=
[
x
for
x
in
expr
.
index
if
x
.
startswith
(
'mt-'
)
or
x
.
startswith
(
'MT-'
)]
if
not
mt_index
:
percent_mt
=
0
else
:
mt_umis
=
expr
.
loc
[
mt_index
,
:].
sum
(
axis
=
0
)
mt_umis
=
expr
.
loc
[
pd
.
Series
(
mt_index
)
,
:].
sum
(
axis
=
0
)
percent_mt
=
mt_umis
/
total_num_UMIs
percent_mt
=
percent_mt
.
replace
(
np
.
inf
,
0
)
...
...
celseq2/template/config.yaml
View file @
1839866a
...
...
@@ -23,6 +23,10 @@ STAR: '/absolute/path/to/star'
## Whare is the directory to save STAR index?
STAR_INDEX_DIR
:
'
/absolute/path/to/star/folder/'
## Extra parameters to run aligner. For example:
## '--outSAMmultNmax 1 --outFilterScoreMinOverLread 0.3'
ALIGNER_EXTRA_PARAMETERS
:
'
'
####################################
## Annotations ##
####################################
...
...
celseq2/workflow/celseq2_beta.snakemake
View file @
1839866a
...
...
@@ -43,6 +43,8 @@ BOWTIE2_INDEX_PREFIX = config.get('BOWTIE2_INDEX_PREFIX', None)
BOWTIE2 = config.get('BOWTIE2', None) # '/local/apps/bowtie2/2.3.1/bowtie2'
STAR_INDEX_DIR = config.get('STAR_INDEX_DIR', None)
STAR = config.get('STAR', None)
ALIGNER_EXTRA_PARAMETERS = config.get('ALIGNER_EXTRA_PARAMETERS', '')
## Annotations ##
# '/ifs/data/yanailab/refs/danio_rerio/danRer10_87/gtf/Danio_rerio.GRCz10.87.gtf.gz'
GFF = config.get('GFF', None)
...
...
@@ -345,20 +347,21 @@ if ALIGNER == 'bowtie2':
sam = join_path(DIR_PROJ, SUBDIR_ALIGN_ITEM,
'{itemID}', ALIGNER+'.bigsam'),
params:
threads = num_threads
threads = num_threads,
aligner_extra_parameters = ALIGNER_EXTRA_PARAMETERS,
log:
join_path(DIR_PROJ, SUBDIR_LOG, '{itemID}',
'Align-Bowtie2.log')
run:
shell(
"""
{BOWTIE2
}
\
-p {params.threads
}
\
-x {BOWTIE2_INDEX_PREFIX
}
\
-U {input.fq} \
-S {output.sam} 2>{log
}
\
--seed 42
"""
)
cmd = '{BOWTIE2} '
cmd += '-p {params.threads} '
cmd += '-x {BOWTIE2_INDEX_PREFIX
}
'
cmd += '-U {input.fq
}
'
cmd += '-S {output.sam
}
'
cmd += '--seed 42 '
cmd += '{params.aligner_extra_parameters
}
'
cmd += '2>{log} '
shell(cmd
)
if ALIGNER == 'star':
rule align_star:
...
...
@@ -377,9 +380,10 @@ if ALIGNER == 'star':
star_prefix = join_path(DIR_PROJ, SUBDIR_ALIGN_ITEM,
'{itemID}', '.star', ''),
threads = num_threads,
aligner_extra_parameters = ALIGNER_EXTRA_PARAMETERS,
run:
mkfolder(params.star_prefix)
cmd = 'STAR '
cmd = '
{
STAR
}
'
cmd += ' --runRNGseed 42 '
cmd += ' --genomeLoad NoSharedMemory '
cmd += ' --runThreadN {params.threads} '
...
...
@@ -388,6 +392,7 @@ if ALIGNER == 'star':
cmd += ' --readFilesIn {input.fq} '
cmd += ' --outFileNamePrefix {params.star_prefix} '
# cmd += ' --outSAMmultNmax 1 '
cmd += ' {params.aligner_extra_parameters} '
shell(cmd)
starsam = join_path(params.star_prefix, 'Aligned.out.sam')
...
...
docs/about/release_note.md
View file @
1839866a
...
...
@@ -10,6 +10,17 @@
---
## :fa-flag-checkered: **v0.5.2**
:fa-calendar:
**2018-04-16**
:fa-star:
**Features**
-
Generate QC plots for UMI-counts matrices. If ST is performed, an extra QC plot masked on grid is generated.
-
Allow experienced users to feed extra parameters to align. See issue #10.
---
## :fa-flag-checkered: **v0.5.1**
:fa-calendar:
**2018-04-05**
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment