Comments (10)
Adapter input is "fasta" format.... so
>name
ad1
>name
ad2
Original comment by [email protected]
on 20 Jun 2011 at 6:38
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Original comment by [email protected]
on 20 Jun 2011 at 8:37
- Added labels: Priority-Low, Type-Other
- Removed labels: Priority-Medium, Type-Defect
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Original comment by [email protected]
on 20 Jun 2011 at 8:38
- Changed state: Invalid
- Added labels: Priority-Medium, Type-Defect
- Removed labels: Priority-Low, Type-Other
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Also, it only reports the adapters found. So if you pass 20 of them, it will
only report the 3 or 4 it finds.
Original comment by [email protected]
on 21 Jun 2011 at 1:57
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[deleted comment]
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In my opinion this issue should be re-open as "valid" and addressed. One of
the adapter in my example is actually a real illumina adapter and fastq-mcf had
failed to recognize it. The abitrariness of your "filtering" is worrisome.
Original comment by [email protected]
on 21 Jun 2011 at 3:23
from ea-utils.
If you can give me an example of where an adapter should be clipped, that would
be OK. I believe the adapter was "real"... it's filtered if it's not found
in the fastq file in significant numbers.
Original comment by [email protected]
on 11 Jan 2012 at 5:39
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[deleted comment]
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I'm going to close this issue, only because it's old, and I can't reproduce it
reliably. I did greatly increase the sampling window to fix a number of issues
people have seen where they were concerned with undetected adapters, however at
some point, the benefits outweigh the risks of false-positive clipping.
Original comment by [email protected]
on 10 May 2012 at 4:04
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Original comment by [email protected]
on 31 May 2012 at 1:41
- Changed state: WontFix
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Related Issues (20)
- sam-stats doesn't support -o and -O option HOT 3
- Incorrect total reads when using FIFO HOT 2
- fastq-mcf: invalid adapter file ==> Floating point exception HOT 1
- The gtf2bed script generate bed with wrong chrStart and chrEnd coordinates for plus strand HOT 4
- Limit on the number of files it can handle HOT 1
- fastq-multx when barcode is in header between # and / symbols? HOT 7
- fastq-multx supporting sequence in header HOT 1
- Compilation on Mac HOT 2
- Giant FASTQ support in stats HOT 3
- Wrong number (/ counter / calculation) in summary statistics of fastq-mcf HOT 2
- fastq-mcf not working correctly on ubuntu 14.04 HOT 9
- error message: "fastq-mcf has stopped working" HOT 4
- gtf2bed wrong output. HOT 1
- compilation error because sparsehash/sparse_hash_map is not found HOT 1
- "fastq-mcf has stopped working"
- Patches for porting ea-utils to other POSIX platforms + warnings clean-up HOT 1
- Use fastq-mcf with methylation data HOT 2
- installing ea-utils on windows7 HOT 1
- gsl_randist.h: No such file or directory HOT 1
- Support for detecting fixed-length prefix barcodes for fastq-multx
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