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Search: Posts Made By: syfo
Forum: Bioinformatics 11-18-2014, 05:10 AM
Replies: 1
Views: 2,344
Posted By syfo
That sounds like CAGE. I suggest you take a look...

That sounds like CAGE. I suggest you take a look at the work from Piero Carninci's group (RIKEN), in one of their papers I think they identified several types of TSS "peaks". Look for Timo Lassman,...
Forum: Bioinformatics 10-14-2014, 07:08 AM
Replies: 6
Views: 2,363
Posted By syfo
I'm curious about this one: IDBA-Hybrid: an...

I'm curious about this one: IDBA-Hybrid: an iterative De Bruijn Graph De Novo Assembler for hybrid sequencing...
Forum: Bioinformatics 09-02-2014, 04:30 AM
Replies: 8
Views: 4,467
Posted By syfo
On a side note, you can use the "samtools view...

On a side note, you can use the "samtools view -c" option instead of counting "yourself" the number of lines.
Forum: Bioinformatics 09-01-2014, 02:26 AM
Replies: 2
Views: 2,381
Posted By syfo
If you have read alignments in bam format on the...

If you have read alignments in bam format on the one hand and a gene annotation in gtf/gff/bed format on the other hand it should be simple to compare both with bedtools.

For instance something...
Forum: Bioinformatics 08-29-2014, 01:51 AM
Replies: 4
Views: 1,902
Posted By syfo
Hi, thanks for your help. Well, in my case...

Hi, thanks for your help.

Well, in my case I precisely do not want samtools to use the reference sequence for the calling, I am looking for the consensus from the reads only.

Also, most of...
Forum: Bioinformatics 08-28-2014, 05:28 AM
Replies: 4
Views: 1,902
Posted By syfo
Same here. Ns in the consensus fasta while the...

Same here.
Ns in the consensus fasta while the region seems to be well covered. I guess it is about some quality filtering but I do not manage to get the right parameters.
Anyone with a...
Forum: Bioinformatics 08-25-2014, 01:24 AM
Replies: 4
Views: 1,313
Posted By syfo
Bedtools proposes a bamToFastq...

Bedtools proposes a bamToFastq (http://bedtools.readthedocs.org/en/latest/content/tools/bamtofastq.html) too.
Forum: Bioinformatics 08-18-2014, 07:49 AM
Replies: 2
Views: 1,700
Posted By syfo
If you are looking for reference-free SNP calling...

If you are looking for reference-free SNP calling -forgive me if I've read too quickly- you might try KisSnp (http://link.springer.com/chapter/10.1007%2F978-3-642-16321-0_14) and/or take a look at...
Forum: Bioinformatics 08-18-2014, 07:41 AM
Replies: 4
Views: 1,604
Posted By syfo
The bam format is designed to represent genomic...

The bam format is designed to represent genomic alignments of sequencing reads. Such alignments are typically generated by mapping reads on the genome with tools like star, bwa, etc. Since you have...
Forum: Bioinformatics 08-18-2014, 04:18 AM
Replies: 4
Views: 1,283
Posted By syfo
I'd try with bedtools. Something like converting...

I'd try with bedtools. Something like converting the gff to bed, generate a bed file with 500Kb genomic bins, run bedtools intersect or coverage to get the overlap in each bin and parse the resulting...
Forum: Bioinformatics 08-13-2014, 08:54 AM
Replies: 12
Views: 3,365
Posted By syfo
concise mode: cat input | awk...

concise mode:

cat input | awk '/^>/{$1=">"++n"\n"substr($1,2)}1'
Forum: Bioinformatics 08-11-2014, 08:34 AM
Replies: 1
Views: 1,215
Posted By syfo
A tricky point is to define the precise criteria...

A tricky point is to define the precise criteria you want to consider (what do you mean exactly by "the percentage of length covered for each gene" or "a percentage of variability"?). A measure that...
Forum: Bioinformatics 08-11-2014, 06:30 AM
Replies: 14
Views: 2,640
Posted By syfo
which gives you more explicitly: awk...

which gives you more explicitly:

awk 'NR==FNR{des[">"$1]=$0;next}/^>/ && des[$1]{$0=">"des[$1]}1' annotation_file fasta_file > output-file.txt
Forum: Bioinformatics 08-11-2014, 06:28 AM
Replies: 14
Views: 2,640
Posted By syfo
Just redirect the default output into a file by...

Just redirect the default output into a file by adding at the end of the command something like

> name-of-your-output-file.txt
Forum: RNA Sequencing 08-05-2014, 05:19 AM
Replies: 4
Views: 3,205
Posted By syfo
Yes, that is a limitation of most RNA-seq...

Yes, that is a limitation of most RNA-seq technologies. As long as RNA fragmentation is required you can never be sure that a given read comes from the transcript it maps to. It can come from another...
Forum: RNA Sequencing 08-05-2014, 02:36 AM
Replies: 4
Views: 3,205
Posted By syfo
I am not sure to see what you mean by "retrieve...

I am not sure to see what you mean by "retrieve 3'UTRs" exactly. Is the goal to improve the existing gene annotation (by extending the annotated 3'UTRs for instance)?

Also,

Since polyAs are...
Forum: Bioinformatics 08-01-2014, 01:56 AM
Replies: 14
Views: 2,640
Posted By syfo
That simple awk command works fine: awk...

That simple awk command works fine:
awk 'NR==FNR{des[">"$1]=$0;next}/^>/ && des[$1]{$0=">"des[$1]}1' annotation_file fasta_file

cat annotation_file
comp1558_c0_seq1 repressor protein...
Forum: RNA Sequencing 07-17-2014, 02:32 AM
Replies: 7
Views: 2,646
Posted By syfo
Right, Cufflinks does not require the data to...

Right, Cufflinks does not require the data to come from coding mRNAs and will work as (good or bad as) usual. I think the specificity of the pipeline is after the RNA-seq data mapping/assembling....
Forum: Bioinformatics 07-17-2014, 02:01 AM
Replies: 2
Views: 2,793
Posted By syfo
Unless your RNA-seq protocol was targeting non...

Unless your RNA-seq protocol was targeting non coding or small RNAs, you are mostly sequencing mRNAs that have been spliced (typically the case if rRNAs have been filtered out using polyA selection),...
Forum: RNA Sequencing 07-15-2014, 08:40 AM
Replies: 7
Views: 2,646
Posted By syfo
You could ask the people who did the GENCODE...

You could ask the people who did the GENCODE annotation, they must have a specific pipeline for lncRNAs. Make sure at least to take a careful look at the paper if not done already (Thomas Derrien et...
Forum: Bioinformatics 07-15-2014, 08:32 AM
Replies: 2
Views: 1,014
Posted By syfo
This looks like the "whole gene" description...

This looks like the "whole gene" description format, which is not what you want here.
- Go back to the UCSC Table Browser.
- Select Mammal / Human / hg19 / Genes / UCSC genes (for example) /...
Forum: Personalized Genomics 08-19-2013, 06:28 AM
Replies: 109
Views: 92,820
Posted By syfo
Efficient identification of Y chromosome...

Efficient identification of Y chromosome sequences in the human and Drosophila genomes (http://genome.cshlp.org/content/early/2013/08/06/gr.156034.113.abstract)

Notwithstanding their biological...
Forum: Bioinformatics 07-15-2013, 05:15 AM
Replies: 1
Views: 765
Posted By syfo
Regarding your first question (I am not sure I...

Regarding your first question (I am not sure I understand the others) about numbering the first base, the answer depends on the format: in BED files the first nucleotide is assigned a "0" while in...
Forum: Bioinformatics 07-08-2013, 03:06 AM
Replies: 7
Views: 6,872
Posted By syfo
A short one: awk '/^>/{$0=$0"_"(++i)}1'...

A short one:

awk '/^>/{$0=$0"_"(++i)}1' infile
Forum: General 07-04-2013, 06:41 AM
Replies: 3
Views: 9,472
Posted By syfo
This looks relevant too: Synthetic spike-in...

This looks relevant too:
Synthetic spike-in standards for RNA-seq experiments. (http://www.ncbi.nlm.nih.gov/pubmed/21816910)
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