User: mastal511

gravatar for mastal511
mastal5111.7k
Reputation:
1,720
Status:
Trusted
Location:
Last seen:
6 hours ago
Joined:
1 year, 7 months ago
Email:
m********@gmail.com

Posts by mastal511

<prev • 247 results • page 1 of 25 • next >
0
votes
0
answers
60
views
0
answers
Comment: C: bowtie -n aligment mode
... the seed length is just a 'seed' or starting point for the alignment. ...
written 6 hours ago by mastal5111.7k
1
vote
1
answer
168
views
1
answers
Comment: C: How does regularized log transformed data from DESeq2 relate to read counts?
... It's not the P-values that are on the log2 scale, it's the number of counts. ...
written 19 days ago by mastal5111.7k
2
votes
1
answer
142
views
1
answers
Answer: C: Bam file with unmapped reads from another genome than reference
... Map your reads to hg19 first, remove the reads that map, then align the unmapped reads to the viral genome. ...
written 4 weeks ago by mastal5111.7k
1
vote
2
answers
327
views
2
answers
Comment: C: Visualising indexed and sorted bam files
... You can use the Broad Institute's IGV to look at the data. ...
written 10 weeks ago by mastal5111.7k
1
vote
0
answers
372
views
0
answers
Comment: C: DeSeq2 MA plot
... What version of DESeq 2 are you using? Note that the MA plots shown in the current DESeq2 vignette plot res or resLFC, and you are plotting dds. Link to DESeq2 vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html ...
written 4 months ago by mastal5111.7k
0
votes
0
answers
159
views
0
answers
Comment: C: How to find and download the Database from a particular gene in NCBI
... Sounds like the OP is maybe referring to metagenomics? ...
written 4 months ago by mastal5111.7k
1
vote
4
answers
246
views
4
answers
Answer: A: Compare pairs of key/value of perl hash tables
... You could iterate through one hash, and for each gene ID (location) key in the hash, check if it is present in the other hash, and whether the values are the same, and print out the Location and Position when you find matching values. But you would have to make hashes of arrays, because hash keys i ...
written 4 months ago by mastal5111.7k
0
votes
1
answer
334
views
1
answers
Answer: A: FastQC and adapters
... If you are referring to the FastQC per base sequence content plots, it depends on what type of data you have. For RNA-Seq data the pattern you see for the first n bases is thought to be due to the random-priming not being quite so random. I think also for Nextera data, the transposase may be biased ...
written 5 months ago by mastal5111.7k
4
votes
1
answer
210
views
1
answers
Answer: C: Read length difference between the analysis type and true reads
... The explanation for having one base more than expected (e.g. 101 instead of 100), is that for Illumina data, the phasing for each position in the read depends also on the data from the next base, so the last base in the read will always have a much worse base quality, because there is no data from a ...
written 5 months ago by mastal5111.7k
0
votes
0
answers
280
views
0
answers
Comment: C: duplicate read names in TCGA raw bam file
... I've had the opposite problem (bedtools bamtofastq did not give the required results, Picard tools did the job), but with single end data, so I don't know what would happen for paired-end reads. The bam files had multiple entries for some of the reads, which were multi-mappers. With bedtools bamtof ...
written 5 months ago by mastal5111.7k

Latest awards to mastal511

Scholar 4 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 4 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 5 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Weird fastq format
Scholar 5 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Weird fastq format
Scholar 9 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Scholar 10 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 10 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Guru 10 months ago, received more than 100 upvotes.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Scholar 12 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Voter 13 months ago, voted more than 100 times.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Scholar 17 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Scholar 17 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 18 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Centurion 18 months ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 956 users visited in the last hour