User: marongiu.luigi

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Germany, Mannheim, UMM
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Posts by marongiu.luigi

<prev • 459 results • page 1 of 46 • next >
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Answer: C: Error in extracting SRA file: symbol lookup error
... Does not matter. I reinstalled all SRAtoolkit and now it works... case closed. ...
written 4 days ago by marongiu.luigi520
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Error in extracting SRA file: symbol lookup error
... Hello I am trying to extract fastq files from SRA files. I used the remote command fastq-dump --split-files SRR9649373 and also manually downloaded the SRA file and then ran the local command fastq-dump -I --split-files SRR9649373.1 but in both cases I get the error: fastq-dump: ...
software error next-gen sequence written 4 days ago by marongiu.luigi520
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How to calculate the occurrence of a stretch of nucleotides in a genome?
... Is there a simple formula to calculate the probability of finding a given sequence of nucleotides in a target sequence? I have seen this formula: a = (g/2)^G+C × ((1-g)/2)^A+T, where: a = probability g = G+C content of the target genome C+G = number of G and C in the stretch A ...
genome written 10 days ago by marongiu.luigi520
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Comment: C: makeblastdb check for correct formatting
... I got this: $ blastdbcheck -db ~/Documents/Transposons/GRCh38.fa -dbtype nucl -full Writing messages to at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. TaxID testing is DISABLED. Using `full' mode: every OID will be tested. Testing 1 vol ...
written 5 weeks ago by marongiu.luigi520
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Comment: C: makeblastdb check for correct formatting
... Yes, I am using a program that calls blast internally and I am getting errors such as `[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.` and `FileNotFoundError: [Errno 2] No such file or directory: '/home/gigiux/Documents/Transposons/Results/A0N-vs-Human endogenous ...
written 5 weeks ago by marongiu.luigi520
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makeblastdb check for correct formatting
... hello, I made a blast database with makeblastdb -in GRCh38.fa -dbtype nucl -out GRCh38.fa the execution is fine but is there a way to check if the formatting is correct? Thank you ...
software error sanity check blastdb written 5 weeks ago by marongiu.luigi520 • updated 5 weeks ago by GenoMax95k
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Comment: C: How to run Transeq?
... OK, so I can omit the last parameter. But what are `fasta` and `fastafile`? In the example it is said `"L1s"` and `/home/L1s.fasta` but these files are not in the folder associated with Transeq... ...
written 12 weeks ago by marongiu.luigi520
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How to run Transeq?
... Hello, I would like to use [Transposeq][1] for the analysis of transposition in human sequences. I ran the following command: RUN_TRANSPOSEQ.sh NORdedup.bam TUMdedup.bam N-samp T-samp "19" containingFolder containingFolder 27 90 5 fasta fastafile queue & where: RUN_TRANSPOSEQ.sh = exe ...
software error use sequencing written 12 weeks ago by marongiu.luigi520
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How to be sure that the microbiome I obtained is sound?
... Hello, I have carried out a virome study from human samples. I have removed the sequences with below 33 phred-score, I ran BLASTN and BLASTX and removed everything that gave bacterial outcome to concentrate on viral sequences. The sequences I got do not result in the species reported as contaminant ...
assembly next-gen error alignment sequencing written 4 months ago by marongiu.luigi520
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Answer: A: how to download all reference files with ensembl and taxon ID?
... I have found it: esearch -db "nucleotide" -query "txid10239 [Organism] AND refseq[filter]" | efetch -format fasta > ref.fa Case closed. ...
written 4 months ago by marongiu.luigi520

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