seq.txt, qseq.txt and fastq

[NicoBxl]

Hi,

What is the difference betweend seq.txt format, qseq.txt format and fastq format ?

Thanks

N.

[feixue1039]

As I know, the difference between fastq format and fasta format is that each base in the fastq file has a quality value which can tell you whether the base call is reliable.The fasta format discard this quality value information.

I hope it will help you.

[mathew]

.fastq and .txt files

Hi
I have kind of similar question- I am not clear what is the difference in seq file .fastq and .txt file of same seq. The problem I have is our inhouse run normally use .txt file When I check fastq file and .txt file they appear to be same.


Am i missing something.
Thanks


here is snap shot of .txt
@HWI-ST550_0128:8:1101:1400:2026#CCGTCC/1
NTTTTCAAAATAGCAAAAACTCTTTGAAGTTAAACATTAAGAAAATGCTAA
+HWI-ST550_0128:8:1101:1400:2026#CCGTCC/1
BP\cceeegggggihhiiiiiiiiiheggiiiiiiihiiihiihiiiiiif
@HWI-ST550_0128:8:1101:1297:2085#CCGTCC/1


and fastq

@HWI-ST550_0128:8:1101:1187:2009#ATGTNN/1
NGTTTGTTTGAATTTATGAGTTAGGTCCATCAACCTAGGCTGATATTNNGA
+HWI-ST550_0128:8:1101:1187:2009#ATGTNN/1
BP\cceceggeeehhfgheghghihgihhhgfgfgd^eghhhegffhBBBB
@HWI-ST550_0128:8:1101:1162:2025#AGTTNN/1
NTACATTTATAATGTAACATGTGTAACATTATACACATATCTCTTTGNNTC
+HWI-ST550_0128:8:1101:1162:2025#AGTTNN/1

[pbluescript]

fastq is just a type of text file. It refers to the format of the sequence data, which looks fine in your examples.

[bbm]

Anybody know how to convert qseq to fasta or fastq?
thanks!

[westerman]

From the QIIME manual (easily found via a web search):

You can convert qseq files to fastq files using the process_qseq.py script.