I was talking to Paul the other day. He has some Illumina reads that look like they still have adapter sequence in them. I think he wants to trim out the adapter sequences from the fastq file which would leave some reads shorter than others. This is why reads of different length are in the same file (at the moment)
Variable Length Reads In De Novo Assembly
Hi Are there any de novo assemblers that will allow for variable length reads in one input file?
I have rna-seq transcriptome data and want remove adaptors (or parts of them) found in each read. The only way I can think of doing this is to remove the adaptors and write them back to a file. The problem is that there will be a range of read lengths in this file. I was hoping to avoid having to split this file into seperate files each containing same length reads. Hopefully this makes sense. Apologies for not explaining more clearly.
• 5,398 views
•
link
updated
by
Ryan Thompson
•
written
by
Pauln •
•
written
by
Pauln •
4 answers
We used the Newbler assembler (454/Roche) to assemble transcriptome reads from several different platforms (454, Sanger, and Illumina). Reads from these platforms are of different lengths.
Is it a requirement that the reads be in a single input file? The Newbler assembler will accept multiple input files.
mira3 will also permit the assembly of different length fragments. Depending on what you need exactly, they may have to be in different files. (ex: 454 vs sanger)
• 8 views
•
link
written
by
Eric Normandeau
You may have to pool your sequences into separate files based on length. Let's say you started with 100-bp reads, and you trimmed variable overlaps of an adapter sequence off of them. You could put all the full-length ones in one file, all the 90-99bp ones in another file, 80-89bp ones in another, and so on down the the smallest you can use (30bp or so?). Then you can use an assembler that accepts different sizes in different files.
• 0 views
•
link
written
by
Ryan Thompson
Log in to answer this question.
More posts like this
-
Read length for single -ended RNA seq data analysis
written by vinaya •
-
Trimmomatic before or after or nope for genome guided assembly?
written by slin023 •
-
Efficient way to perform fastq filtering of contaminants by read name prior to transcriptome assemb…
written by jfaberha •
-
Best method to assemble low-abundance transcripts?
written by molly77 •
-
Can a part of a read be in the alignment and in the supplementary alignment (-F 0x800) as well?
written by Matteo Schiavinato
-
Concatenate F read files & concatenate R read files in attempts for improved transcriptome?
written by jammydodger123456 •
-
Best statistical validity for RNAseq from FFPE samples at different read lengths
written by achimbell •
-
Should I trim both R1 and R2 if only R2's quality is poor?
written by lakhujanivijay
-
RNA-Seq de novo assembly: split ion proton read sequences
written by jules.augley •
-
Aligner For Mapping Mate Pair (Outies) Data
written by Abhi
do you mean variable-trimmed reads or reads from different sequencers (sanger, illumina, 454)
do you mean variable quality-trimmed reads or reads from different sequencers (sanger, illumina, 454)?
Hi @paulN For this question, as well as for any next ones, it would be good to detail things a bit more. What is your starting material? What are you trying to accomplish? What are some limitations, assumptions? You will thus get much better answers and they will be more usefull to others too. Cheers!