Tag: fq.gz

Secret BBMAP helper page – HRGV/Marmics_Metagenomics Wiki

#How to map to the assembled scaffolds.fasta bbmap is a powerful and highly flexible read mapper jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/. For the upcoming analysis you are not interested in the typical mapping output but in statistics on the coverage on every scaffold, you can get them with scaffstats. We want to be specific…

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Trimmomatic parameters

Trimmomatic parameters 0 $java -jar /apps/eb/Trimmomatic/0.39-Java-1.8.0_144/trimmomatic-0.39.jar PE -phred33 seq1_L2_1.fq.gz seq1_L2_2.fq.gz _L2_r1_paired_fq.gz seq1_L2_r1_unpaired.fq.gz seq_L2_r2_paired.fq.gz Seq1_L2_r2_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5 Trimmomatic • 137 views • link updated 15 hours ago by GenoMax 110k • written 17 hours ago by ronny • 0 Login before adding your…

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Using STAR SJ.out.tab file to identify novel ncRNAs

Using STAR SJ.out.tab file to identify novel ncRNAs 0 Hi All, I am attempting to identify novel ncRNAs from a circadian RNAseq dataset. Specifically I have a ribo-depleted RNAseq timecourse with 31 samples (sample every 2 hours for 60hrs). I have run STAR (code below). I am trying to follow…

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STAR+RSEM pippline without gtf

STAR+RSEM pippline without gtf 0 Dear all, I have question I mapped reads on cds sequence through STAR I don’t have gtf file and want to calculate read count using RSEM but I am stuck by error “RSEM error: RSEM currently does not support gapped alignments” as I don’t have…

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BBMerge / Tadpole error correction

I’ve been using BBMerge recently to address a very specific problem: I am sequencing pooled short DNA molecules (< 400bps) using paired end reads (average length ~ 230 bps post trimming) Each molecule can be assumed to be different (i.e. contains sequence differences – substitutions & indels – with respect…

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How to pass custom software specific variables to nf-core/sarek nextflow pipeline?

How to pass custom software specific variables to nf-core/sarek nextflow pipeline? 0 I’m attempting to call whole genome variants using nf-core/sarek nextflow pipeline. In QC step there is an option that invokes trim_galore quality trimming, but i don’t know how to pass my custom adapters to be cut as well….

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STAR align multiple files

STAR align multiple files 1 Hi everybody, I am doing alignment to 36 PE samples using star. to make it little bit easy task I wrote a bash loop to align them all with the same command. here is my loop: for i in $(ls raw_data); do STAR –genomeDir index.150…

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Biostar Systems

Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 That is good to know that it isn’t just my set of reads…still concerning, though. Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 I was not expecting this — not sure what to make of it…

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question about running CIRI-full

question about running CIRI-full 1 I’m using ciri-full to calculate the full length sequence of circRNAs ,and I can run the test data set successfully, but I can’t run my own data running test data set: java -jar ../CIRI-full.jar Pipeline -1 test_1.fq.gz -2 test_2.fq.gz -a test_anno.gtf -r test_ref.fa -d test_output/…

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I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv.

I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv. 0 Hey everyone, before i start apologies for the inconvenience cause of my wrong or inappropriate use of terms. I take some fails of bwa mem lately. As i…

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