Moderator: h.mon

gravatar for h.mon
h.mon29k
Reputation:
29,160
Status:
Trusted
Location:
Brazil
Last seen:
16 minutes ago
Joined:
7 years, 5 months ago
Email:
h***********@gmail.com

about me

Posts by h.mon

<prev • 4,084 results • page 1 of 409 • next >
1
vote
1
answer
82
views
1
answers
Answer: A: How to annotate edgeR results?
... The annotation is available at the Rice Sheath Blight Pathogen Genomics Database download page ([here][1]). You then have to format the gene set of interest into some format the functional enrichment software you want to use - for example, here is a list of formats Broad GSEA accepts: [Data formats] ...
written 21 hours ago by h.mon29k
0
votes
2
answers
102
views
2
answers
Answer: A: RNA read alignment using transcriptome
... The command should be the same as for building a reference genome index. However, as far as I know, hisat2 hasn't been widely used for this, the commonly used alternatives being bwa or bowtie2. ...
written 5 days ago by h.mon29k
0
votes
1
answer
116
views
1
answers
Comment: C: How does the parameter "number_of_threads" work in MIRA?
... >Is this due to my machine's lack of processing power? What are you machine specs? MIRA is very resource hungry, and excess sequencing coverage can cause an explosion of memory consumption. The manual recommends down-sampling to ~100x coverage. ...
written 5 days ago by h.mon29k
0
votes
1
answer
134
views
1
answers
Comment: C: ClustalX2 guide tree
... You are indeed correct. I have updated my answer. ...
written 6 days ago by h.mon29k
0
votes
2
answers
117
views
2
answers
Comment: C: Finding the cause for corrupt ChIP-Seq data
... It seems like not only he aligned R1 and R2 separately, but also did the quality and adapter trimming separately for R1 and R2. ...
written 7 days ago by h.mon29k
1
vote
0
answers
103
views
0
answers
Comment: C: how to merge two big file faster
... It is clear, it is immediately above the manual snippet I pasted above: >HUMAnN2 and paired-end sequencing data > >End-pairing relationships are currently not taken into account during HUMAnN2's alignment steps. This is due to the fact that HUMAnN2 strictly aligns reads to isolated coding ...
written 7 days ago by h.mon29k
0
votes
0
answers
103
views
0
answers
Comment: C: how to merge two big file faster
... I would reserve the term merging to when R1 and R2 are merged based on their overlap, as this is the currently adopted practice. Keep in mind: 1. you are throwing out information when you concatenate the files (although it is true metaphlan2 and humann2 do not use this information). 2. these con ...
written 9 days ago by h.mon29k
0
votes
0
answers
103
views
0
answers
Comment: C: how to merge two big file faster
... What are you merging? `read1.fq` and `read2.fq` are the forward and reverse reads of a sequencing run? Why are you merging them? What are the downstream analyses you want to perform? ...
written 10 days ago by h.mon29k
0
votes
1
answer
76
views
1
answers
Answer: A: How do I convert a flow file (.FLOW) into fastq file.
... You need more than just the flow values to be able to get a fastq file. The flow values, by themselves, just encodes the number of homopolymer runs of the called nucleotide, but they do not contain information about which nuceotide it is. Typically, 454 output is a `.sff` file, a binary file contai ...
written 10 days ago by h.mon29k
0
votes
2
answers
98
views
2
answers
Comment: C: Small RNA length distribution
... Show the commands used for trimming and mapping. miRNAs sequencing should be enriched for ~18-26bp reads, both because this is their typical length when mature, and because (correct) library preparation should preferentially select this range. However, it is common to have a large proportion of pi ...
written 12 days ago by h.mon29k

Latest awards to h.mon

Scholar 1 day ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Appreciated 1 day ago, created a post with more than 5 votes. For C: Kraken2 vs Minimap2 and Blast results seem to be incongruent
Appreciated 3 days ago, created a post with more than 5 votes. For C: Kraken2 vs Minimap2 and Blast results seem to be incongruent
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Appreciated 9 weeks ago, created a post with more than 5 votes. For Benchmarking bioinformatics tools
Appreciated 9 weeks ago, created a post with more than 5 votes. For Benchmarking bioinformatics tools
Scholar 10 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Why does BWA sometimes omit X0 and X1 tags?
Scholar 3 months ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
Scholar 3 months ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Why does BWA sometimes omit X0 and X1 tags?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Are all RPKM/FPKMs in RNAseq "equal" ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Why does BWA sometimes omit X0 and X1 tags?
Scholar 3 months ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Why does BWA sometimes omit X0 and X1 tags?
Scholar 3 months ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: STAR align multiple files
Scholar 4 months ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
Scholar 4 months ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: STAR align multiple files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1951 users visited in the last hour