featureCount
最后发布时间 : 2023-05-09 00:02:19
浏览量 :
featureCounts \
-B -C \
-p \
-g gene_id \
-t exon \
--countReadPairs \
-T 10 \
-a genome.gtf \
-s 0 \
-o M5.gene_id.featureCounts.txt \
M5.sorted.bam
参数说明
-s: Perform strand-specific read counting. A single integer value (applied to all input files) or a string of comma- separated values (applied to each corresponding input file) should be provided. Possible values include: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). Default value is 0 (ie. unstranded read counting carried out for all input files).-B: Only count read pairs that have both ends aligned.-C: Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.
New parameter '--countReadPairs' is added to featureCounts to explicitly specify that read pairs will be counted, and the '-p' option in featureCounts now only specifies if the input reads are paired end (it also implied that counting of read pairs would be performed in previous versions).
注意在subread2.0.2以上的版本中-B参数不起作用，需要使用--countReadPairs
HISAT2 summary stats:
Total pairs: 11358194
Aligned concordantly or discordantly 0 time: 3028860 (26.67%)
Aligned concordantly 1 time: 7950038 (69.99%)
Aligned concordantly >1 times: 219881 (1.94%)
Aligned discordantly 1 time: 159415 (1.40%)
Total unpaired reads: 6057720
Aligned 0 time: 3587203 (59.22%)
Aligned 1 time: 2364281 (39.03%)
Aligned >1 times: 106236 (1.75%)
Overall alignment rate: 84.21%
(7950038+219881)*2 = 16339838
featureCounts -t exon \
-g gene_id \
--primary \
-s 0 \
-p \
-T 24 \
-a resources/genome.gtf \
-o gwat_ABX_OLZ_18.featureCounts \
results/hisat2/gwat_ABX_OLZ_18/hisat2.bam
featureCounts(2.0.3)
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ | __ | ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== ___ | | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ | |____ / ____ | |__| |
========== |_____/ ____/|____/|_| _______/_/ ______/
v2.0.3
//========================== featureCounts setting ===========================\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| hisat2.bam ||
|| ||
|| Output file : gwat_ABX_OLZ_18.featureCounts ||
|| Summary : gwat_ABX_OLZ_18.featureCounts.summary ||
|| Paired-end : yes ||
|| Count read pairs : no ||
|| Annotation : genome.gtf (GTF) ||
|| Dir for temp files : ./ ||
|| ||
|| Threads : 24 ||
|| Level : meta-feature level ||
|| Multimapping reads : not counted ||
|| Multiple alignments : primary alignment only ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\============================================================================//
//================================= Running ==================================\
|| ||
|| Load annotation file genome.gtf ... ||
|| Features : 526640 ||
|| Meta-features : 30560 ||
|| Chromosomes/contigs : 48 ||
|| ||
|| Process BAM file hisat2.bam... ||
|| Paired-end reads are included. ||
|| The reads are assigned on the single-end mode. ||
|| Total alignments : 23750177 ||
|| Successfully assigned alignments : 12709161 (53.5%) ||
|| Running time : 0.05 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
|| Summary of counting results can be found in file "gwat_ABX_OLZ_18.feature ||
|| Counts.summary" ||
|| ||
\============================================================================//
samtools view results/hisat2/gwat_ABX_OLZ_18/hisat2.bam | wc -l
23750177
featureCounts参数--countReadPairs结果
featureCounts -t exon \
--countReadPairs \
-g gene_id \
--primary \
-s 0 \
-p \
-T 24 \
-a resources/genome.gtf \
-o gwat_ABX_OLZ_18.featureCounts \
results/hisat2/gwat_ABX_OLZ_18/hisat2.bam
featureCounts(2.0.3)
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ | __ | ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== ___ | | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ | |____ / ____ | |__| |
========== |_____/ ____/|____/|_| _______/_/ ______/
v2.0.3
//========================== featureCounts setting ===========================\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| hisat2.bam ||
|| ||
|| Output file : gwat_ABX_OLZ_18.featureCounts ||
|| Summary : gwat_ABX_OLZ_18.featureCounts.summary ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : genome.gtf (GTF) ||
|| Dir for temp files : ./ ||
|| ||
|| Threads : 24 ||
|| Level : meta-feature level ||
|| Multimapping reads : not counted ||
|| Multiple alignments : primary alignment only ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\============================================================================//
//================================= Running ==================================\
|| ||
|| Load annotation file genome.gtf ... ||
|| Features : 526640 ||
|| Meta-features : 30560 ||
|| Chromosomes/contigs : 48 ||
|| ||
|| Process BAM file hisat2.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 11973112 ||
|| Successfully assigned alignments : 5785413 (48.3%) ||
|| Running time : 0.08 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
|| Summary of counting results can be found in file "gwat_ABX_OLZ_18.feature ||
|| Counts.summary" ||
|| ||
\============================================================================//
featureCounts -t exon \
-g gene_id \
--primary \
-s 0 \
-p \
-T 24 \
-B \
-a resources/genome.gtf \
-o gwat_ABX_OLZ_18.featureCounts \
results/hisat2/gwat_ABX_OLZ_18/hisat2.bam
featureCounts(2.0.1)
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ | __ | ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== ___ | | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ | |____ / ____ | |__| |
========== |_____/ ____/|____/|_| _______/_/ ______/
v2.0.1
//========================== featureCounts setting ===========================\
|| ||
|| Input files : 1 BAM file ||
|| o hisat2.bam ||
|| ||
|| Output file : gwat_ABX_OLZ_18.featureCounts ||
|| Summary : gwat_ABX_OLZ_18.featureCounts.summary ||
|| Annotation : genome.gtf (GTF) ||
|| Dir for temp files : ./ ||
|| ||
|| Threads : 24 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : not counted ||
|| Multiple alignments : primary alignment only ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : required ||
|| ||
\============================================================================//
//================================= Running ==================================\
|| ||
|| Load annotation file genome.gtf ... ||
|| Features : 526640 ||
|| Meta-features : 30560 ||
|| Chromosomes/contigs : 48 ||
|| ||
|| Process BAM file hisat2.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 11973112 ||
|| Successfully assigned alignments : 5785413 (48.3%) ||
|| Running time : 0.08 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
|| Summary of counting results can be found in file "gwat_ABX_OLZ_18.feature ||
|| Counts.summary" ||
|| ||
\============================================================================//
小数据实例
featureCount(2.0.3)
featureCounts -t exon \
-g gene_id \
--primary \
-s 0 \
-p \
-T 24 \
-a genome/genome.gtf \
-o 220613-95 \
output/hisat2/220613-95.bam
//================================= Running ==================================\
|| ||
|| Load annotation file genome.gtf ... ||
|| Features : 526640 ||
|| Meta-features : 30560 ||
|| Chromosomes/contigs : 48 ||
|| ||
|| Process BAM file 220613-95.bam... ||
|| Paired-end reads are included. ||
|| The reads are assigned on the single-end mode. ||
|| Total alignments : 250 ||
|| Successfully assigned alignments : 124 (49.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
|| Summary of counting results can be found in file "220613-95.summary" ||
|| ||
\============================================================================//
samtools view -c output/hisat2/220613-95.bam
250
featureCount(2.0.1)
featureCounts -t exon \
-g gene_id \
--countReadPairs \
--primary \
-s 0 \
-p \
-T 24 \
-a genome/genome.gtf \
-o 220613-95 \
output/hisat2/220613-95.bam
//================================= Running ==================================\
|| ||
|| Load annotation file genome.gtf ... ||
|| Features : 526640 ||
|| Meta-features : 30560 ||
|| Chromosomes/contigs : 48 ||
|| ||
|| Process BAM file 220613-95.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 125 ||
|| Successfully assigned alignments : 63 (50.4%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
|| Summary of counting results can be found in file "220613-95.summary" ||
|| ||
\============================================================================//