Masurca assemble questions

Question

[tigerhui587]

Hi,

I have two questions about using masurca to assemble plant genome.

1. Do I need to reverse complement the jump library before assembling? It says #reverse (R2) reads are optional for PE libraries and mandatory for JUMP libraries, but it seems no flag to specify this.
2. After I execute 'assemble.sh', I got some errors:

[Sat Jun 13 16:39:50 CDT 2015] Processing pe library reads
[Sat Jun 13 16:39:54 CDT 2015] Processing sj library reads
Average PE read length 1
choosing kmer size of 31 for the graph
cat: write error: Broken pipe
MIN_Q_CHAR: 33
[Sat Jun 13 17:44:04 CDT 2015] Creating mer database for Quorum.
[Sat Jun 13 17:53:42 CDT 2015] Error correct PE.
Cutoff computation failed. Pass it explicitly with -p switch.
Error correction of PE reads failed. Check pe.cor.log.

And there is no 'pe.cor.log' file. I don't know how to fix this. Hope somebody can help me! Thanks a lot.

Best regards,
Hui

Answer 1

[arnstrm]

For the first question, it simply means that you can either provide a single-end reads or paired end reads with the PE flag, where as with the JUMP flag, you always provide a mate pair library (must have R1 and R2). Although there is a FRG flag, you can't supply single-end reads with that, AFAIK. No, you don't have to reverse complement the reads. PE will assume the reads are facing each other (innies) and JUMP will assume reads are facing out (outies).

Second question, not exactly sure what it means (cutoff computation failed). I think it failed to get a value for the MIN_Q_CHAR in the assemble.sh script. Try running the single line on the terminal to see why it is failing (it could be because you might have specified the input files in correctly)

[tigerhui587]

Hi arnstrm,

Where is the FRG flag? I didn't see it anywhere. Do you think my config file is okay? Thank you!

DATA
PE= pe 476 60 DNA-1_CGATGT_L002_R1_001_paired_trimmed_paired_1.fastq.normalized_K25_C30_pctSD200.fq DNA-1_CGATGT_L002_R1_001_paired_trimmed_paired_2.fastq.normalized_K25_C30_pctSD200.fq
JUMP= sh 7000 1000 PBU1-7k_CCGTCC_L005_R1_001_paired_trimmed_paired_1.fastq.normalized_K25_C30_pctSD200.fq PBU1-7k_CCGTCC_L005_R1_001_paired_trimmed_paired_2.fastq.normalized_K25_C30_pctSD200.fq
END