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1500 questions
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3 answers

sort a fasta file containing the Oxford Nanopore Technologies (ONT) header by sequencing start_time ascending

I have basecalled ONT reads and converted them to multifasta. The multifasta contains the original ONT headers in this format: 3ebb56cd-3671-4abd-b1ac-0c759bt068d0 runid=eb6214851489c8e00eb0dcbd00d737f7dddxxxx read=1078 ch=422…
andresito
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RcppArmadillo installation error

When I am trying to install the RcppArmadillo Bioconductor library in R, it is giving me the following error: /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status make: *** [RcppArmadillo.so] Error 1 ERROR: compilation…
Nikita Vlasenko
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2 answers

Can we use non base-called fast5 files in poretools?

I run the MinION MinKNOW without the live base-calling option. We know there is Metrichor and Albacore to perform base-calling after this process. However, I have not done any base-calling yet. My question is: Is it possible to use directly the…
andresito
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1 answer

SPAdes error during assembly

I try to perform a hybrid assembly using Unicycler. Unicycler use SPAdes to assembly the illumina sequences, and the program crashes while in SPAdes. The spades.log file says something about an invalid argument and error code 22. I have run the…
5norre
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1 answer

Scaffolding a genome with hybrid data

I am assembling a ~500MB genome, and have ~150x long reads and ~200x 150bp PE short reads, with a ~400bp insert size. I've done a lot of work with minimap+miniasm, and have what I think is a good set of unitigs and a .gfa file from miniasm.…
roblanf
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2 answers

Identifying relevant SNPs from a list

I have a list of all SNPs (a list of RsIDs) that fall in the coding sequence of several thousand human genes, and I'm looking for a convenient method to come up with a list of known SNPs that alter an amino acid in those genes. I'll be glad to hear…
Adrian Smith
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1 answer

Automating sequence download from Wormbase

I'm working on the C. elegans model organism, for which there exists an online biological information database: Wormbase. I'm able to manually search for a transcript (say "K06C4.12") and this gets me the following…
bli
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How to submit a canu job on LSF high-performance computing cluster farm?

I am currently running canu on an LSF Linux server using the following script called assemble.sh: canu -p species -d output genomeSize=100m -pacbio-raw subreads.fastq I then submit this script with the following in a computer node: bsub -q basement…
Biomagician
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1 answer

What algorithms exist for reverse protein folding?

Are there any algorithms already in existence for reverse protein folding/docking (e.g. taking a desired surface map/docking profile and generating DNA which will produce a protein to fold into it?) Protein folding seems straightforward (though…
CoryG
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1 answer

Integration of different microarray dataset to run GSEA

I'm planning to run a GSE Analysis on some microarray datasets. Until now what I have done is to pre-processed them using frma algorithm. The reason I chose frma instead of gcrma or rma is that I wanted to merge these different dataset into…
J. Doe
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2 answers

EMT/EMT-like processes in bioinformatics to study cancer progression

First I am not sure why, but it seems EMT can be used to infer the status of cancer progression. What kind of databases are there for the EMT process in the context of cancer? I saw this book which mentions ArrayExpress, but I need some help to…
0x90
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Large range parameter identification

I have a model (ODE) of an enzymatic reaction, and I'd like to estimate four of its parameters to fit some available data. To obtain the model I am just using Mass-Action Kinetics. Some more details: The model is of the form…
PepeToro
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3
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1 answer

problem of "ordering in physical positions" phasing SNPs with Shapeit

I'm trying to phase my data (whole genome resequencing SNPs) with Shapeit (from ped file) and I get this error message : [33mERROR:[0m Wrong ordering in physical positions curr_pos=54 prev_pos=65 I found that it's due to the fact that my .map file…
G. Dumont
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1 answer

IMPUTE2 missing filter option

I went through the manuals and can't find the meaning of the below flag: -filt_rules_l 'filter==0' Here is the link to manual for this flag: filt_rules_l Can anyone explain? IMPUTE version: impute_v2.3.1_x86_64_dynamic Edit: The full IMPUTE2…
zx8754
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Quantification of EST/cDNA based retained intron transcripts

Note: this question has also been asked on Biostars We are seeing a retained intron transcript event for some RNAseq samples, and we want to assess at the sequence level which intron retention events are actually occurring so that we can do protein…
Martin
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