Apologies for the long content..


I seem to be having a discrepancy with fastx_collapser as well. 

I have converted from s_8_sequence_clipped.fa to s_8_sequence_collapsed.fa

fastx_collapser -v -i s8_sequence_clipped.fa -o s8_sequence_collapsed.fa
Input: 26580941 sequences (representing 212647528 reads)    --->  what the..?
Output: 3177400 sequences (representing 212647528 reads)

In my collapsed file, my top read is: 
>1-35820208
TACCTGGTTGATCCTGCCAGTAG

(this is already over my original read count)

When I 

grep -e TACCTGGTTGATCCTGCCAGTAG -c s_8_sequence_clipped.fa 
4,503,566

....

Ok, I've reanalyzed a previous dataset and the output is consistent with my previous numbers:

fastx_collapser -v -i s3-sequence.fa -o s4-sequence-RETEST.fa
Input: 36008043 sequences (representing 36008043 reads)
Output: 3886503 sequences (representing 36008043 reads)

so it doesn't appear to be the toolkit.

How are the tools counting "reads" and "sequences" ?
Could the format of the headers affect it? hyphens vs underscores? 

This data set:
>ILLUMINA-08A740_0000:8:1:1736:1055#0/1
GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGA

Previous data set:
>GAPC_0034_FC:1:1:1548:1028#0/1
AAACTTCATCGTTATCGAGCGA


Thanks

From: keneclip@hotmail.com
To: galaxy-user@bx.psu.edu
Date: Thu, 14 Apr 2011 00:54:05 +0000
Subject: [galaxy-user] regarding read counts from fastx_clipper

Hi, 

I'm using the fastx_toolkit (v0.0.13) command line scripts. 

When using fastx_clipper, I get: 

fastx_clipper -a TCGTATGCCGTCTTCTGCTTG -v -c -l 15 -M 5 -i s_8_sequence.fa -o s_8_sequence_clipped.fa
Clipping Adapter: TCGTATGCCGTCTTCTGCTTG
Min. Length: 15
Non-Clipped reads - discarded.
Input: 227673720 reads.
Output: 212647528 reads.
discarded 3527200 too-short reads.
discarded 725608 adapter-only reads.
discarded 10773384 non-clipped reads.
discarded 0 N reads.

The s_8_sequence.fa file is 2.2Gb, s_8_sequence_clipped.fa file is 1.7Gb.... seems like fastx_clipper is reporting way too many reads in this instance.  
I also tried without the -M option but same thing. 

I checked with:

wc -l s_8_sequence.fa
56918430
(divide this by 2 gives 28,459,215 reads)

wc -l s_8_sequence_clipped.fa
53161882
(divided by 2 gives 26,580,941 reads)


There has never been such a discrepancy with this tool. 

I'm not sure if I'm doing something silly this time round, or somethings changed in my system that's affecting fastx_clipper counting. 

Heres a couple of lines from input and output:

head -n 6 s_8_sequence.fa
>ILLUMINA-08A740_0000:8:1:1736:1055#0/1
GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGA
>ILLUMINA-08A740_0000:8:1:2219:1057#0/1
CAAGCGTCGGAGGTTTAGTCTTTCGTATGCCGTCTTCTGC
>ILLUMINA-08A740_0000:8:1:2316:1056#0/1
TACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTG

head -n 6 s_8_sequence_clipped.fa
>ILLUMINA-08A740_0000:8:1:2219:1057#0/1
CAAGCGTCGGAGGTTTAGTCTT
>ILLUMINA-08A740_0000:8:1:2316:1056#0/1
TACCTGGTTGATCCTGCCAGTAG
>ILLUMINA-08A740_0000:8:1:3041:1059#0/1
GAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA


Any ideas? 

Thanks, 

Ken

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