User: marongiu.luigi
marongiu.luigi • 520
- Reputation:
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- Germany, Mannheim, UMM
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- 4 days, 17 hours ago
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Posts by marongiu.luigi
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... Does not matter. I reinstalled all SRAtoolkit and now it works... case closed. ...
written 4 days ago by
marongiu.luigi • 520
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... 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: ...
written 4 days ago by
marongiu.luigi • 520
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... 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 ...
written 10 days ago by
marongiu.luigi • 520
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... 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.luigi • 520
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... 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.luigi • 520
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... 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 ...
written 5 weeks ago by
marongiu.luigi • 520
• updated
5 weeks ago by
GenoMax ♦ 95k
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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.luigi • 520
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... 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 ...
written 12 weeks ago by
marongiu.luigi • 520
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... 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 ...
written 4 months ago by
marongiu.luigi • 520
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... 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.luigi • 520
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