Should you specify “-p” for paired end reads using featureCounts?
I’m trying to understand whether or not I should be using the -p
flag for featureCounts
.
Here’s the explanation:
-p If specified, fragments (or templates) will be counted
instead of reads. This option is only applicable for
paired-end reads; single-end reads are always counted as
reads
Here’s the output with and without the flag:
# Program:featureCounts v2.0.1; Command:"/expanse/projects/jcl110/anaconda3/envs/VEBA-assembly_env/bin/featureCounts" "-a" "veba_output/assembly/SRR5720299/intermediate/1__assembly/scaffolds.fasta.saf" "-o" "featurecounts.tsv" "-F" "SAF" "--tmpDir" "veba_output/assembly/SRR5720299/tmp/featurecounts" "-T" "1" "veba_output/assembly/SRR5720299/intermediate/2__alignment/mapped.sorted.bam"
Geneid Chr Start End Strand Length veba_output/assembly/SRR5720299/intermediate/2__alignment/mapped.sorted.bam
SRR5720299__NODE_1_length_71757_cov_11.4961 SRR5720299__NODE_1_length_71757_cov_11.4961 1 71757 + 71757 11519
SRR5720299__NODE_2_length_69346_cov_13.9814 SRR5720299__NODE_2_length_69346_cov_13.9814 1 69346 + 69346 13008
SRR5720299__NODE_3_length_55956_cov_13.3612 SRR5720299__NODE_3_length_55956_cov_13.3612 1 55956 + 55956 10725
SRR5720299__NODE_4_length_53799_cov_18.5165 SRR5720299__NODE_4_length_53799_cov_18.5165 1 53799 + 53799 12722
SRR5720299__NODE_5_length_48507_cov_9.1492 SRR5720299__NODE_5_length_48507_cov_9.1492 1 48507 + 48507 6543
SRR5720299__NODE_6_length_45224_cov_17.2711 SRR5720299__NODE_6_length_45224_cov_17.2711 1 45224 + 45224 10538
SRR5720299__NODE_7_length_41565_cov_12.9338 SRR5720299__NODE_7_length_41565_cov_12.9338 1 41565 + 41565 8035
SRR5720299__NODE_8_length_41525_cov_13.7932 SRR5720299__NODE_8_length_41525_cov_13.7932 1 41525 + 41525 7738
(base) [jespinoz@exp-15-06 TestVEBA]$
(base) [jespinoz@exp-15-06 TestVEBA]$ head featurecounts.paired.tsv
# Program:featureCounts v2.0.1; Command:"/expanse/projects/jcl110/anaconda3/envs/VEBA-assembly_env/bin/featureCounts" "-a" "veba_output/assembly/SRR5720299/intermediate/1__assembly/scaffolds.fasta.saf" "-o" "featurecounts.paired.tsv" "-F" "SAF" "--tmpDir" "veba_output/assembly/SRR5720299/tmp/featurecounts" "-T" "1" "-p" "veba_output/assembly/SRR5720299/intermediate/2__alignment/mapped.sorted.bam"
Geneid Chr Start End Strand Length veba_output/assembly/SRR5720299/intermediate/2__alignment/mapped.sorted.bam
SRR5720299__NODE_1_length_71757_cov_11.4961 SRR5720299__NODE_1_length_71757_cov_11.4961 1 71757 + 71757 5801
SRR5720299__NODE_2_length_69346_cov_13.9814 SRR5720299__NODE_2_length_69346_cov_13.9814 1 69346 + 69346 6573
SRR5720299__NODE_3_length_55956_cov_13.3612 SRR5720299__NODE_3_length_55956_cov_13.3612 1 55956 + 55956 5411
SRR5720299__NODE_4_length_53799_cov_18.5165 SRR5720299__NODE_4_length_53799_cov_18.5165 1 53799 + 53799 6386
SRR5720299__NODE_5_length_48507_cov_9.1492 SRR5720299__NODE_5_length_48507_cov_9.1492 1 48507 + 48507 3322
SRR5720299__NODE_6_length_45224_cov_17.2711 SRR5720299__NODE_6_length_45224_cov_17.2711 1 45224 + 45224 5330
SRR5720299__NODE_7_length_41565_cov_12.9338 SRR5720299__NODE_7_length_41565_cov_12.9338 1 41565 + 41565 4111
SRR5720299__NODE_8_length_41525_cov_13.7932 SRR5720299__NODE_8_length_41525_cov_13.7932 1 41525 + 41525 3892
Using paired-end method, it’s ~2x without the paired-end method but not exact.
My questions:
-
Why isn’t -p run 2X of a run without -p? Is it because only one read in the pair aligns in some cases?
-
Would it be a safe bet to just set -p for all my paired-end runs?
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