aechchiki
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1 answers
8 votes
6k views
Extracting expression data from GSE dataset downloaded from GEO
8 votes

According to the manual, all you need to do is: library('GEOquery') gseGSE16146 <- getGEO('GSE16146', GSEMatrix=FALSE) As explanation, getGEO() outputs by default to GSEMatrix=TRUE and returns a ...

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2 answers
5 votes
588 views
full visualisation of draft genomes alignment
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6 votes

Found a solution, using D-Genies, worked great. Some examples from their website: Thanks to @user172818.

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1 answers
3 votes
402 views
Cufflinks Error: sort order of reads in BAMs must be the same
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6 votes

Just add --dta-cufflinks to your Hisat2 command, so that the output alignment file provides the attributes needed by Cufflinks (XS flags). This should do the job. From manual: Report alignments ...

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1 answers
5 votes
103 views
What format is this? Pretty sure it's not a BED file
6 votes

It looks like a weird way to represent data. You're right, it does not at all look like a BED. Digging in GEO made me find this information: Supplementary_files_format_and_content: Tab-delimited ...

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5 answers
2 votes
725 views
How to measure the total size of a fastq file in base pairs?
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5 votes

I've been using this: cat file.fastq | paste - - - - | cut -f 2 | tr -d '\n' | wc -c Explanation : paste - - - - : print four consecutive lines in one row (tab delimited), to merge the info for each ...

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1 answers
2 votes
421 views
Salmon tximport
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5 votes

You are right, samples.txt is not generated by Salmon (or any other transcript abundance quantifiers). From documentation, you can find a link to an example of how samples.txt should look like. Note:...

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1 answers
3 votes
2k views
How to find novel transcripts using GFFcompare?
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4 votes

The output of gffcompare includes several files per run (just like cuffcompare). Example for a run: $ ls cuffcmp.* | sed 's/\t/\n/' cuffcmp.combined.gtf cuffcmp.loci cuffcmp.output.gtf.refmap cuffcmp....

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3 answers
7 votes
2k views
visualisation of genome alignment
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4 votes

After a bit of digging, finally found exactly what I was looking for. I'll share here in case someone else was looking for the same thing. I used a standard Nucleotide BLAST (blastn), coupled with ...

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2 answers
8 votes
7k views
Converting a BAM file into VCF
4 votes

You can use Freebayes, provided you have your BAM file and the reference genome. Example: freebayes -f genome.fa aln.bam > var.vcf I'd suggest you go through the whole github documentation, and ...

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5 answers
5 votes
7k views
How to extract / convert gff3 CDS sequences to multifasta
4 votes

The gffread utility in Cufflinks package might be interesting for you. To generate a multi-fasta file with nucleotide sequences from your GFF file, then you can try: gffread -w output_transcripts....

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2 answers
4 votes
277 views
Is there a way to quickly verify the presence of some SNPs in Fastq files?
4 votes

Try this pipeline: Clean raw fastq files (trimmomatic) Align clean fastq files to the reference genome (dna-to-dna aligner of your choice) Convert the alignment sam file to bam (samtools) Call SNPs ...

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2 answers
3 votes
173 views
Produce a single sequential FASTA sequence out of BAM
3 votes

If you just want the human chromosomes in a FASTA format, why not downloading directly the individual chromosome files (chr*.fa.gz)? If you don't rely on the "official" releases (for whatever reason)...

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1 answers
0 votes
318 views
What is a standard approach to binarize microarray gene expression data?
2 votes

Based on the info you provide, ArrayBin R package provides you the necessary tools: binarize.array() from ArrayBin, allowing: Implementation of an adaptive method for binarizing gene expression ...

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1 answers
3 votes
528 views
gffread: GFaSeqGet errors on coordinate overhang
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2 votes

Basically, the source of the problem is issues with hard/soft clipped bases in short-reads RNAseq reads alignments to reference genome in post-transcriptome assembly steps. Truncating the ...

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1 answers
6 votes
330 views
PASA pipeline: compare experimental transcripts to the reference annotation
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2 votes

Answer from the authors: PASA ends up using gff3 format instead of sam format for uploading the alignments. If somebody has the gmap gff3 output, then can be done to just upload that directly ...

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2 answers
4 votes
1k views
How to get Nanopore MinION fast5 from SRA
2 votes

I would suggest trying an alternative way, as the FAST5 is a fairly new entry in SRA - 6 public datasets as of today. You can search the ERX/ERR entry you got from SRA in ENA and either (1) direct ...

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4 answers
1 votes
268 views
At what processing step should library strandedness type be taken into account?
2 votes

I usually take into account library strandness during the mapping to the reference step (but I never worked with bigwig files myself). Assuming RNA-seq data from Illumina, you can use Hisat2 for ...

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2 answers
5 votes
588 views
full visualisation of draft genomes alignment
1 votes

Also, Mashmap has an embedded visualisation tool generating dot-plots to visualize mappings, ideal for: highly similar species or to compare different assemblies of the same species. mapping genome ...

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2 answers
4 votes
222 views
Exon-exon junctions: compare experimental transcripts to reference annotation
1 votes

For future googlers, Ding et al., 2017 published a review: "Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data". Table 1 has the list of software in this review.

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1 answers
2 votes
144 views
Is it possible to find out the PacBio chemistry from the PacBio Sequel BAM's header?
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1 votes

According to PacBio Sequel BAM format manual, you can find information on the chemistry version in the header entries @RG (read group), tag DS (description), entry BASECALLERVERSION . In case of ...

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1 answers
2 votes
388 views
Mark BWA-SW split alignments in output for long reads
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1 votes

From BWA manual, it is advised to use BWA-MEM in your longs read case (unless you have a good reason not to): BWA-MEM and BWA-SW share similar features such as long-read support and split alignment,...

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2 answers
6 votes
557 views
Is it wise to use RepeatMasker on prokaryotes?
1 votes

From your comment, it seems that masking regions are not your priority, but you would rather find them (correct me if I am wrong): not interested in masking, but really finding any type of repeats, ...

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4 answers
8 votes
100 views
Introduce errors in reference transcripts according to external dataset error model
1 votes

The executable fastq-sim in DNemulator package is able to modify a set of input sequences in fasta format according to an external set of quality scores reported in a fastq file.

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1 answers
0 votes
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Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)
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0 votes

A comment from a Nextclade's user satisfies my actual needs, I will post it here for future reference: Hi - one possible source is the metadata file for UCSC’s daily-updated tree of public SARS-CoV-2 ...

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