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Search: Posts Made By: Jane M
Forum: Bioinformatics 05-10-2019, 01:13 AM
Replies: 2
Views: 636
Posted By Jane M
Thank you for your feedback. The concept of...

Thank you for your feedback.
The concept of this pilot study is very interesting but it seems that 3 years later, there was no new development unfortunately.
The principle of data privacy is...
Forum: Bioinformatics 05-02-2019, 07:47 AM
Replies: 2
Views: 636
Posted By Jane M
Lists of somatic mutations from WGS

Dear all,

I am looking for lists of somatic mutations from cohorts of patient (>=50 patients).
There are some discussions about this search (https://www.biostars.org/p/217812/), but I did not...
Forum: Bioinformatics 08-21-2017, 06:53 AM
Replies: 0
Views: 1,050
Posted By Jane M
Question MSIsensor parameters

Dear all,

I am using MSIsensor for the first time.
As a first test, I launched it on my paired (realigned, recalibrated) bam files using default parameters and got the output files without...
Forum: Bioinformatics 08-18-2017, 08:37 AM
Replies: 1
Views: 1,256
Posted By Jane M
If it can help someone in the future, we can get...

If it can help someone in the future, we can get this type of information on NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/
In *_report.txt files, for each contigs, there is...
Forum: Bioinformatics 08-17-2017, 08:06 AM
Replies: 1
Views: 1,256
Posted By Jane M
Question Extracting alternate loci from fasta genome

Dear all,

I downloaded full reference fasta genomes for hg19, mm9 and mm10 from gencode. They include reference chromosomes, scaffolds, assembly patches and haplotypes.
For a specific purpose, I...
Forum: Bioinformatics 11-25-2016, 12:43 AM
Replies: 0
Views: 1,107
Posted By Jane M
Question Visualize unionBedGraphs file in UCSC

Dear all,

I have generated bedgraphs that I can visualize in UCSC. For example:
head BIO_31-T1-ARN.bedGraph
track type=bedGraph name=BIO_31-T1-ARN
chr5 170000000 170000600 0.00...
Forum: Bioinformatics 07-26-2016, 01:31 AM
Replies: 4
Views: 2,198
Posted By Jane M
Thank you for your answer. I am working on a...

Thank you for your answer.

I am working on a sh screen. The first 22-30 bases are common to all sequences. Between 23 and 31 bases correspond to the sh in each sequence.
Since there is a problem...
Forum: Bioinformatics 07-24-2016, 11:56 PM
Replies: 4
Views: 2,198
Posted By Jane M
Thank you Brian for your suggestion. I am doing...

Thank you Brian for your suggestion.
I am doing some tests with Bowtie on shorter sequences and if it doesn't work, I will try BBMap. The maximum length I can use is 23 bp. Would it be sufficient?
Forum: Bioinformatics 07-21-2016, 02:55 AM
Replies: 4
Views: 2,198
Posted By Jane M
Question Allowing a high number of mismatches when mapping

Dear all,

I have sequences of 53bp, among which between 23 and 30 bases are of interest (=motifs). For simplicity, I took only the first 17 bases. Each sample has between 5 and 23 millions of...
Forum: RNA Sequencing 05-17-2016, 06:02 AM
Replies: 0
Views: 964
Posted By Jane M
Study of lncRNA: LNCipedia, NONCODE, MiTranscriptome, ...

Hello everybody,

Did some of you use lncRNA databases in addition to Gencode annotation to count reads in genes?
I heard about MiTranscriptome, which contains ~58,000 lncRNA, and is based only on...
Forum: RNA Sequencing 05-12-2016, 06:26 AM
Replies: 11
Views: 2,101
Posted By Jane M
I was actually using only the refFlat gtf from...

I was actually using only the refFlat gtf from UCSC. It looks like what I showed.
I added the refGene and knownGenes gtf files to show that these files do not contain description neither.
There...
Forum: RNA Sequencing 05-12-2016, 05:35 AM
Replies: 11
Views: 2,101
Posted By Jane M
Well, there is no description in the tables I...

Well, there is no description in the tables I downloaded from UCSC. Otherwise, I could indeed check as I did with Genecode annotation. Here are some file header:

refFlat file (RefSeq), that I used...
Forum: RNA Sequencing 05-11-2016, 06:17 AM
Replies: 11
Views: 2,101
Posted By Jane M
Compared to how I ran htseq-count previously, I...

Compared to how I ran htseq-count previously, I added -i option to get counts for each gene_name and not gene_ID. I could run htseq count on this new gtf without any problem :D

htseq-count...
Forum: RNA Sequencing 05-11-2016, 01:46 AM
Replies: 11
Views: 2,101
Posted By Jane M
Thank you again. No problem yet, since I did not...

Thank you again. No problem yet, since I did not try to count. Looking at the file: now, I have ~56600 different gene names, compared to ~26600 with refFlat. The file contains twice more lines....
Forum: RNA Sequencing 05-11-2016, 12:21 AM
Replies: 11
Views: 2,101
Posted By Jane M
Thank you dpryan for your answer. Don't...

Thank you dpryan for your answer.


Don't you thing this refFlat reference is sufficient for experiments with polyA RNA selection?



Since I am working with hg19 annotation, I downloaded the...
Forum: RNA Sequencing 05-10-2016, 12:52 AM
Replies: 11
Views: 2,101
Posted By Jane M
Question Which feature file for htseq-count for non coding elements of ribodepleted samples?

Dear all,

Sorry if this question has been asked before, I have not found similar topics on the web, but there are probably...
Until now, I used a gtf downloaded from UCSC table (genome: human,...
Forum: RNA Sequencing 05-09-2016, 05:15 AM
Replies: 15
Views: 2,940
Posted By Jane M
Still interested in your percentages of remaining...

Still interested in your percentages of remaining rDNA sequence after ribodepletion :D

I have one more question concerning what are the unmapped reads in the ribodepleted experiments. When looking...
Forum: RNA Sequencing 05-02-2016, 05:46 AM
Replies: 15
Views: 2,940
Posted By Jane M
Ok, thank you GenoMax.

Ok, thank you GenoMax.
Forum: RNA Sequencing 05-02-2016, 04:06 AM
Replies: 15
Views: 2,940
Posted By Jane M
Thank you for posting them. I had the...

Thank you for posting them.


I had the impression that 5% was already a good ribodepletion ratio. Let's see if others can give their feedback.




Well, on HiSeq 4000, more than 99% of the...
Forum: RNA Sequencing 05-02-2016, 02:35 AM
Replies: 15
Views: 2,940
Posted By Jane M
I wrote 2 posts last week, they do not appear...

I wrote 2 posts last week, they do not appear (waiting for validation, I don't know why). I hope this one will be posted.



I ran two tests:
1) map the unmapped reads as previously, except I...
Forum: RNA Sequencing 04-28-2016, 06:36 AM
Replies: 15
Views: 2,940
Posted By Jane M
I tried your suggestion on both unmapped and...

I tried your suggestion on both unmapped and mapped reads for one polyA and one ribo sample:





For both runs, I got:
ribo sample:
Forum: RNA Sequencing 04-27-2016, 08:08 AM
Replies: 15
Views: 2,940
Posted By Jane M
Exact Thank you for these suggestions. I...

Exact


Thank you for these suggestions. I will try both, counting the number of reads flagged as optical duplicates and map the unmapped reads to ribosomal DNA, each time in the 2 experiments.
...
Forum: RNA Sequencing 04-27-2016, 06:11 AM
Replies: 15
Views: 2,940
Posted By Jane M
I really appreciate your suggestions GenoMax,...

I really appreciate your suggestions GenoMax, thank you



I used TopHat2 with default parameters:


I was wondering if something was happening with duplicates based on some tests:
One polyA...
Forum: RNA Sequencing 04-27-2016, 05:20 AM
Replies: 15
Views: 2,940
Posted By Jane M
Thank you Chipper for your help. Are these...

Thank you Chipper for your help. Are these sequences present in hg38?
Is it possible to test this hypothesis without mapping the whole transcriptome to hg38?
Forum: RNA Sequencing 04-27-2016, 05:14 AM
Replies: 15
Views: 2,940
Posted By Jane M
Thank you fanli for your suggestion. I used the...

Thank you fanli for your suggestion.
I used the Web BLAST interface on the first "polyA" and "ribo" unmapped reads using "Genome (all assemblies top level)" as database and default settings.
1/10...
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