Should you specify “-p” for paired end reads using featureCounts?

Should you specify “-p” for paired end reads using featureCounts?

0

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?


fastq


rnaseq


genomics

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