User: roberto.spreafico

Reputation:
10
Status:
New User
Location:
United States
Last seen:
3 years, 11 months ago
Joined:
4 years, 3 months ago
Email:
r****************@gmail.com

Posts by roberto.spreafico

<prev • 9 results • page 1 of 1 • next >
0
votes
2
answers
1.6k
views
2
answers
Comment: C: SNP-masking before short-read alignment to human genome
... Thanks Brian, pretty cool, I will give BBMap a try then! Thanks also for all your other suggestions, that is pretty useful! ...
written 4.0 years ago by roberto.spreafico10
0
votes
2
answers
1.6k
views
2
answers
Comment: C: SNP-masking before short-read alignment to human genome
... Thank you Ashutosh, that is very clear and helpful! ...
written 4.0 years ago by roberto.spreafico10
0
votes
2
answers
1.6k
views
2
answers
Comment: C: SNP-masking before short-read alignment to human genome
... Hi Ashutosh, what is your experience with Personal Genome Constructor? Do you see significant improvements over the standard human genome reference? ...
written 4.0 years ago by roberto.spreafico10
0
votes
2
answers
1.6k
views
2
answers
Comment: C: SNP-masking before short-read alignment to human genome
... Thanks Brian! How does BBMap perform with spliced/split reads? Also, will higher sensitivity result in more multimappers that will be eventually discarded, or will precision remain high? Upon trimming reads, what min length do you suggest to retain to avoid reference bias? ...
written 4.0 years ago by roberto.spreafico10
3
votes
2
answers
1.6k
views
2
answers
SNP-masking before short-read alignment to human genome
... Hello I was wondering if somebody has experience with aligning short reads to the reference human genome, and whether masking SNPs improves alignment and decreases reference bias. If masking is advised, how do you choose which SNPs to mask? Would dbSNP with MAF > 1% be a reasonable choice? Do yo ...
reference bias snp human rna-seq written 4.1 years ago by roberto.spreafico10 • updated 12 months ago by Biostar ♦♦ 20
0
votes
2
answers
2.7k
views
2
answers
Comment: C: Reordering the bam file
... Thanks Devon, very clear. In my workflow I rehead a SAM file (with a bash script) to sort SQ header lines as I want. The product is still a SAM file. I then use picard to sort by coordinate (which now forces my SQ header line order) the SAM file, convert to BAM, and index, all together. This seems n ...
written 4.1 years ago by roberto.spreafico10
0
votes
2
answers
2.7k
views
2
answers
Comment: C: Reordering the bam file
... I read this discussion with interest and wished you could clarify a point. Say that you generate an unsorted SAM file. When you invoke picard/samtools to sort by coordinate, the SQ header lines will be used to set how you reorder your reads. If you want a different order, it would make sense to me t ...
written 4.1 years ago by roberto.spreafico10
6
votes
1
answer
1.7k
views
1
answer
Matching Gencode annotations to Assemblies
... Hello, I am trying to match Gencode's annotations to assemblies. It is my understanding that the sequence of reference chromosomes changes only when there is a major version update (e.g. GRCh37 -> GRCh38). For minor versions (such as GRCh38.p2), patches (deltas between the major version and the ...
gtf assembly annotations gencode written 4.1 years ago by roberto.spreafico10 • updated 4.1 years ago by Emily_Ensembl18k
0
votes
0
answers
1.1k
views
0
answers
Equivalence testing RNA-seq with edgeR
... Hi,   I was wondering whether anybody has experience with equivalence testing using edgeR. Usually people are interested in differential expression, and that works out of the box with edgeR. But what if you are interested in genes that do not change in two conditions? Picking those with large p-va ...
tost R rna-seq edger hypothesis testing written 4.3 years ago by roberto.spreafico10

Latest awards to roberto.spreafico

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 931 users visited in the last hour