Hello,
I've run featurecounts and have around ~40% unassigned_fragment
. My reads are paired end 150bp and aligned with STAR (~90-93%
uniquely successfully aligned) and a average read input length of ~299 for all my samples. Here are the conditions I've run for featurecounts and the summary output.
featureCounts \
-p --countReadPairs -B -P \
-F "GTF" \
-J \
-C \
-T 16 \
-g gene_id \
-t exon \
-a $annotation_file \
--extraAttributes "gene_type" \
-o processing/counts/output_file_name \
processing/mapping/star/*.bam
Summary output:
Assigned 14367477 13814907 15921754 14159227 13658284 14979822 15491455 13762178 15848496 13407749 14694807 13113942
Unassigned_Unmapped 0 0 0 0 0 0 0 0 0 0
Unassigned_Read_Type 0 0 0 0 0 0 0 0 0 0
Unassigned_Singleton 0 0 0 0 0 0 0 0 0 0
Unassigned_MappingQuality 0 0 0 0 0 0 0 0 0
Unassigned_Chimera 0 0 0 0 0 0 0 0 0 0
Unassigned_FragmentLength 11617180 10800353 12659685 11053441 11040810 9806741 12528930 11007146
11982978 10008445 11223062 9763096
Unassigned_Duplicate 0 0 0 0 0 0 0 0 0 0
Unassigned_MultiMapping 0 0 0 0 0 0 0 0 0 0
I know that the Unassigned_FragmentLength
could result in the fragments being >600 and <50 from the default settings, but based on the bam summary that is not the case? What else could cause this to happen and how might I resolve it?
Please let me know if there is any other information that would be helpful to resolve this!
Please use the formatting bar (especially the
![code_formatting](https://image.ibb.co/fg0nMx/code_formatting.png)
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.Run without the
-P
flag, does this then include the problematic alignments?