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comments
0
votes
0
replies
323
views
MACS2 parameters slocal and llocal - how are they related to open chromatin?
MACS2
ChIP-Seq
8 months ago by
Pei
▴ 170
1
vote
0
replies
1.2k
views
Answer:
Answer: Differential Gene Expression analysis in Bulk RNA Seq - using Count Matrix as in
8 months ago by
Pei
▴ 170
0
votes
0
replies
403
views
Answer:
Answer: Inferring undisclosed 5mer in proprietary SMARTer oligo sequence
8 months ago by
Pei
▴ 170
0
votes
1
reply
592
views
Answer:
Answer: Whole transcriptome analysis nominated primarily miRNA-related pathways. Advice?
8 months ago by
Pei
▴ 170
1
vote
1
reply
592
views
Answer:
Answer: Whole transcriptome analysis nominated primarily miRNA-related pathways. Advice?
8 months ago by
Pei
▴ 170
0
votes
1
reply
1.1k
views
Comment:
Comment: search for intron conservancy across species
8 months ago by
Pei
▴ 170
0
votes
1
reply
1.1k
views
Answer:
Answer: search for intron conservancy across species
9 months ago by
Pei
▴ 170
0
votes
0
replies
465
views
Annotation of ATAC-seq peak - distal intergenic regions as enhancers
annotation
peak
ATAC-seq
9 months ago by
Pei
▴ 170
0
votes
0
replies
498
views
Comment:
Comment: many more ChIP-seq peaks called in 1 condition than the other
9 months ago by
Pei
▴ 170
3
votes
2
replies
498
views
many more ChIP-seq peaks called in 1 condition than the other
MACS2
ChIP-Seq
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
Pei
▴ 170
0
votes
0
replies
1.4k
views
Comment:
Comment: Are adapter sequences trimmed from ONLY the 3' ends of reads
2.4 years ago by
Pei
▴ 170
4
votes
3
replies
1.4k
views
Are adapter sequences trimmed from ONLY the 3' ends of reads
RNA-SEQ
2.4 years ago by
Pei
▴ 170
1
vote
3
replies
2.2k
views
file size of pair-end sequencing fastq
RNA-SEQ
2.4 years ago by
Pei
▴ 170
0
votes
0
replies
2.2k
views
Comment:
Comment: file size of pair-end sequencing fastq
2.4 years ago by
Pei
▴ 170
0
votes
0
replies
2.2k
views
Comment:
Comment: file size of pair-end sequencing fastq
2.4 years ago by
Pei
▴ 170
0
votes
0
replies
8.1k
views
Comment:
Comment: how to determine a fastq is phred+33 or phred+64
2.4 years ago by
Pei
▴ 170
0
votes
0
replies
8.1k
views
Comment:
Comment: how to determine a fastq is phred+33 or phred+64
2.4 years ago by
Pei
▴ 170
3
votes
4
replies
8.1k
views
how to determine a fastq is phred+33 or phred+64
RNA-seq
phred33
phred64
2.4 years ago by
Pei
▴ 170
0
votes
0
replies
965
views
STAR genomeSAindexNbases
RNA-seq
STAR
mapping
2.4 years ago by
Pei
▴ 170
0
votes
0
replies
3.6k
views
Answer:
A: Mapping left_kept_reads.m2g_um to genome FAILED running Tophat2/Bowtie2
updated 4.3 years ago by
Ram
43k • written 8.2 years ago by
Pei
▴ 170
0
votes
1
reply
4.1k
views
Comment:
C: Should I filter my reads before running bedtools multicov ?
updated 4.4 years ago by
Ram
43k • written 8.4 years ago by
Pei
▴ 170
5
votes
7
replies
4.1k
views
Should I filter my reads before running bedtools multicov ?
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Pei
▴ 170
4
votes
3
replies
2.7k
views
how to improve multiple sequence alignment by removing outlier sequence ?
alignment
updated 4.9 years ago by
Biostar
20 • written 7.7 years ago by
Pei
▴ 170
1
vote
3
replies
1.1k
views
What tool can be used to predct regulatory element within an input sequence ?
sequence
updated 5.2 years ago by
Gautier Richard
▴ 370 • written 5.2 years ago by
Pei
▴ 170
0
votes
0
replies
1.1k
views
Comment:
C: What tool can be used to predct regulatory element within an input sequence ?
5.2 years ago by
Pei
▴ 170
5
votes
2
replies
7.1k
views
tophat, the parameter "Expected inner distance between mate pairs"?
tophat
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Pei
▴ 170
0
votes
1
reply
1.7k
views
Comment:
C: tophat: the Searching for junctions via segment mapping was skipped.
7.8 years ago by
Pei
▴ 170
0
votes
2
replies
1.7k
views
Comment:
A: tophat: the Searching for junctions via segment mapping was skipped.
updated 7.8 years ago by
GenoMax
141k • written 7.8 years ago by
Pei
▴ 170
0
votes
6
replies
1.7k
views
tophat: the Searching for junctions via segment mapping was skipped.
rna-seq
7.8 years ago by
Pei
▴ 170
1
vote
2
replies
3.0k
views
CLIP-seq data process, start from sra file
CLIP
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Pei
▴ 170
1
vote
1
reply
2.3k
views
align RNA-seq reads to annotated CDS
RNA-Seq
7.9 years ago by
Pei
▴ 170
0
votes
1
reply
1.9k
views
Comment:
C: a protein failed to be aligned to genome by tblastn
8.0 years ago by
Pei
▴ 170
1
vote
1
reply
1.9k
views
Answer:
A: a protein failed to be aligned to genome by tblastn
8.0 years ago by
Pei
▴ 170
1
vote
7
replies
1.9k
views
a protein failed to be aligned to genome by tblastn
blast
8.0 years ago by
Pei
▴ 170
0
votes
0
replies
1.9k
views
Comment:
A: a protein failed to be aligned to genome by tblastn
8.0 years ago by
Pei
▴ 170
0
votes
1
reply
1.6k
views
Comment:
C: align two long sequences using Muscle but found gaps only
8.1 years ago by
Pei
▴ 170
0
votes
3
replies
1.6k
views
align two long sequences using Muscle but found gaps only
alignment
8.1 years ago by
Pei
▴ 170
0
votes
1
reply
1.6k
views
Should I remove scaffold when perform tophat and cufflinks ?
rna-seq
updated 8.1 years ago by
Devon Ryan
104k • written 8.1 years ago by
Pei
▴ 170
0
votes
0
replies
1.8k
views
Comment:
Comment: which genome sequence fasta file should be used for builindg bowtie2 index ?
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Pei
▴ 170
3
votes
3
replies
1.8k
views
which genome sequence fasta file should be used for builindg bowtie2 index ?
RNA-Seq
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Pei
▴ 170
0
votes
1
reply
2.5k
views
Comment:
C: low mapping rate when using SRA RNA-seq data
8.2 years ago by
Pei
▴ 170
0
votes
3
replies
2.5k
views
low mapping rate when using SRA RNA-seq data
RNA-Seq
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Pei
▴ 170
0
votes
0
replies
3.1k
views
Comment:
C: How to examine/validate my result of read-count from HTseq-count
8.4 years ago by
Pei
▴ 170
1
vote
2
replies
3.1k
views
How to examine/validate my result of read-count from HTseq-count
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Pei
▴ 170
1
vote
2
replies
2.7k
views
How to annotate a sequence with its genomic coordinates ?
RNA-sequence
coordinates
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
Pei
▴ 170
0
votes
1
reply
1.5k
views
distribution of read-count per gene for results by HTSeq-count
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Pei
▴ 170
0
votes
0
replies
2.4k
views
Comment:
C: when using htseq-count, should I only count read-pairs whose two mates were both
8.4 years ago by
Pei
▴ 170
0
votes
2
replies
2.4k
views
when using htseq-count, should I only count read-pairs whose two mates were both reported ?
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Pei
▴ 170
0
votes
0
replies
1.5k
views
Comment:
C: samtools view run into "uninterruptible sleep" status
8.4 years ago by
Pei
▴ 170
2
votes
2
replies
1.5k
views
samtools view run into "uninterruptible sleep" status
linux
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Pei
▴ 170
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