SPAdes: with different read length

bio_informatics · 06-10-2015, 08:22 AM

Hi members,

I'm facing something weird. I know not all reads in the fastq files can have same length.
But in my trimmed data, read length of reverse and forward files are different. I checked out for only first read, though.

Data: paired end
Organism: E. coli

Output 101 from reverse strand:

Code:

zcat sample_R2_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}'  | head -1

Output 54 from forward strand:

Code:

zcat sample_R1_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}'  | head -1

An icing to this dilemma is, SPAdes uses 55 as K-mer during assembly. And the genome size from assembly is reasonable.

My questions:

1) Shouldn't SPAdes select K-mer less than 55 here?

GenoMax · 06-10-2015, 08:41 AM

Can you tell us why are they different (and uniformly of length 54 for R1)? Did you trim them that way?

bio_informatics · 06-10-2015, 08:48 AM

Hi Genomax,
Thanks for your reply.

I've 2 sets of data, trimmed (sequencing center did this trimming based on the quality)and untrimmed. I used the already trimmed data for assembly.

Oh, they aren't uniform ( looking at already trimmed file).
Have 72 different lengths: max is 101, minimum 30.
So, in a way, all numbers from 30-101 are present for read lengths. That's strange. :-/

GenoMax · 06-10-2015, 08:57 AM

In that case your original question is no longer applicable, correct?

bio_informatics · 06-10-2015, 08:58 AM

Yes.
Sorry.

Quote:

Originally Posted by GenoMax

In that case your original question is no longer applicable, correct?

GenoMax · 06-10-2015, 08:59 AM

No problem. Sounds like you did get a reasonable sized assembly so all should be well.

bio_informatics · 06-10-2015, 09:04 AM

Yes, that is more important.

Merci!

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06-10-2015, 08:22 AM	#1
bio_informatics Senior Member Location: USA Join Date: Nov 2013 Posts: 182	SPAdes: with different read length Hi members, I'm facing something weird. I know not all reads in the fastq files can have same length. But in my trimmed data, read length of reverse and forward files are different. I checked out for only first read, though. Data: paired end Organism: E. coli Output 101 from reverse strand: Code: zcat sample_R2_trimmed.fastq.gz \| awk '{if(NR%4==2) print length($1)}' \| head -1 Output 54 from forward strand: Code: zcat sample_R1_trimmed.fastq.gz \| awk '{if(NR%4==2) print length($1)}' \| head -1 An icing to this dilemma is, SPAdes uses 55 as K-mer during assembly. And the genome size from assembly is reasonable. My questions: 1) Shouldn't SPAdes select K-mer less than 55 here?

06-10-2015, 08:48 AM	#3
bio_informatics Senior Member Location: USA Join Date: Nov 2013 Posts: 182	Hi Genomax, Thanks for your reply. I've 2 sets of data, trimmed (sequencing center did this trimming based on the quality)and untrimmed. I used the already trimmed data for assembly. Oh, they aren't uniform ( looking at already trimmed file). Have 72 different lengths: max is 101, minimum 30. So, in a way, all numbers from 30-101 are present for read lengths. That's strange. :-/ Last edited by bio_informatics; 06-10-2015 at 08:50 AM.

06-10-2015, 08:41 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Can you tell us why are they different (and uniformly of length 54 for R1)? Did you trim them that way?

06-10-2015, 08:57 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	In that case your original question is no longer applicable, correct?

06-10-2015, 08:59 AM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	No problem. Sounds like you did get a reasonable sized assembly so all should be well.

06-10-2015, 09:04 AM	#7
bio_informatics Senior Member Location: USA Join Date: Nov 2013 Posts: 182	Yes, that is more important. Merci!