Question: Fastq joiner and sequencing reads previously submitted to a quality based trimming
0
gravatar for anacrys7
3.6 years ago by
anacrys70
Portugal
anacrys70 wrote:

Hello!

I have a couple of doubts about Fastq joiner:

1) on the Fastq joiner instructions I see that the program will join the paired ends, but will exclude sequences that have lost their pair during quality check. Is there a way of keeping these lone sequences rather than ditching them? 

2) the sequences joining scheme seems to simply concatenate /1 and /2 seqs as they are: shouldn't /2 seqs be reverted? shouldn't they be separated by an N in the middle in the final output?

Input formats

Left-hand Read:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
+HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

Right-hand Read:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR

Output

A multiple-fastq file, for example:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758
GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+HWI-EAS91_1_30788AAXX:7:21:1542:1758

 

Thank a lot by the help!

fastq joiner • 970 views
ADD COMMENTlink modified 3.6 years ago by Anton Nekrutenko1.7k • written 3.6 years ago by anacrys70
0
gravatar for Anton Nekrutenko
3.6 years ago by
Penn State
Anton Nekrutenko1.7k wrote:

One of the assumptions made by the joiner is that the sequences are of the same length. Why are you trying to join sequences?

ADD COMMENTlink written 3.6 years ago by Anton Nekrutenko1.7k
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