command line

[amitpande74]

Hi, I have a GFP and transposon sequence which I want to incorporate for RNASeq analysis. I tried doing this with STAR, but it gives me only the TE sequence alignment and reads in the sb_alignmentsReadsPerGene.out.tab

./generateDecoyTranscriptome.sh [-j <N> =1 default] [-b <bedtools binary path> =bedtools default] [-m <mashmap binary path> =mashmap default] -a <gtf file> -g <genome fasta> -t <txome fasta> -o <output path>

Could you kindly give an explanation for the command line please. Here the exogenous sequences have to be incorporated via the cat command and entries made into the GTF and genome.fasta and txome.fasta ?

I am new to this kind of analysis. Another thing that I found very difficult to do was that if I have to match the coordinates of the BED regions from my DNAseq with the transposon into RNA seq BAM files , I cannot do it via this method of inserting exogenous sequences since it shows the header which we have coined in the input files for the GFP and the TE sequence.

When I ran the analysis:

./generateDecoyTranscriptome.sh -b /usr/local/bin/bedtools -m /home/amit/miniconda3/bin/mashmap -a ../hg19.ncbiRefseq.added.gtf -g ../hg19_added_genes.fa -t ../Homo_sapiens.GRCh38.cdna.all.fa -o /home/amit/Downloads/SalmonTools-master/sb_results
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*** getDecoy ***
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-b <bedtools binary> = /usr/local/bin/bedtools
-m <mashmap binary> = /home/amit/miniconda3/bin/mashmap
-a <Annotation GTF file> = /home/amit/Downloads/SalmonTools-master/hg19.ncbiRefseq.added.gtf
-g <Genome fasta> = /home/amit/Downloads/SalmonTools-master/hg19_added_genes.fa
-t <Transcriptome fasta> = /home/amit/Downloads/SalmonTools-master/Homo_sapiens.GRCh38.cdna.all.fa
-o <Output files Path> = /home/amit/Downloads/SalmonTools-master/sb_results
[1/10] Extracting exonic features from the gtf
[2/10] Masking the genome fasta
[3/10] Aligning transcriptome to genome
>>>>>>>>>>>>>>>>>>
Reference = [reference.masked.genome.fa]
Query = [/home/amit/Downloads/SalmonTools-master/Homo_sapiens.GRCh38.cdna.all.fa]
Kmer size = 16
Window size = 5
Segment length = 500 (read split allowed)
Alphabet = DNA
Percentage identity threshold = 80%
Mapping output file = mashmap.out
Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
Execution threads  = 1
>>>>>>>>>>>>>>>>>>
INFO, skch::Sketch::build, minimizers picked from reference = 937226701
./generateDecoyTranscriptome.sh: line 105: 14872 Segmentation fault      (core dumped) $mashmap -r reference.masked.genome.fa -q $txpfile -t $threads --pi 80 -s 500

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*** ABORTED ***
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An error occurred. Exiting...

Kindly guide.