User: Grinch

gravatar for Grinch
Grinch10
Reputation:
10
Status:
New User
Location:
Sweden
Last seen:
2 weeks, 6 days ago
Joined:
2 years, 11 months ago
Email:
s**********@gmail.com

Posts by Grinch

<prev • 16 results • page 1 of 2 • next >
0
votes
0
answers
156
views
0
answers
Comment: C: samtools idxstats reports zero aligned or unaligned reads
... Bowtie output doesn't give the number of mapped reads per chromosome. I'm actually trying to replicate the data from an article and they claim they have used Bowtie2 for the alignment and after that, they have a script on GitHub which automates the downstream processing. But the script doesn't work ...
written 9 weeks ago by Grinch10
0
votes
0
answers
156
views
0
answers
Comment: C: samtools idxstats reports zero aligned or unaligned reads
... The index was made yesterday and I have also tried re-doing the conversion sam to bam, sorting, and indexing. With samtools view command, i get the number of mapped reads so everything is correct, but still idxstats doesn't want to give me any reads. ...
written 9 weeks ago by Grinch10
0
votes
0
answers
156
views
0
answers
samtools idxstats reports zero aligned or unaligned reads
... I've aligned ChIP-seq data that is publically available (SRP004897), with Bowtie2 -k 3 command. I need information on the number of aligned reads per chromosome for downstream processing, for which I've used samtools idxstats. The output of idxstats shows 0 aligned and 0 unaligned reads, see below: ...
idxstats samtools written 9 weeks ago by Grinch10 • updated 8 days ago by Biostar ♦♦ 20
0
votes
1
answer
128
views
1
answers
Comment: C: How to replace a stretch of a sequence with N's in a fasta file
... That was a simple solution and it worked perfectly. I was overthinking how to solve it. Thank you! ...
written 9 weeks ago by Grinch10
3
votes
1
answer
128
views
1
answer
How to replace a stretch of a sequence with N's in a fasta file
... Hi! I´m trying to change a stretch of 300,000 nucleotides on chromosome 21, with NNN´s in a fasta file. This turned out to be not such a trivial task. I searched BioPython packages for a solution but can't find anything appropriate. It needs to a specific region between 8,202,082–8,552,360 nucleotid ...
fasta biopython written 9 weeks ago by Grinch10 • updated 9 weeks ago by h.mon14k
1
vote
3
answers
825
views
3
answers
Answer: A: database for enhancer sequences in human/mammal genomes
... There are many databases available: EnhancerAtlas: http://enhanceratlas.org/, VISTA https://enhancer.lbl.gov/, FANTOM http://fantom.gsc.riken.jp/5/data/, DenDB: http://www.cbrc.kaust.edu.sa/dendb/ ...
written 14 months ago by Grinch10
0
votes
1
answer
504
views
1
answers
Answer: A: fastQC - case of the anomalous last base
... Hi, my first thought is, was your sample treated in any way or do you have any overrepresented sequences? If the bias is only at the final base, than it's most probably due to too aggressive adapter trimming, or due to your trimming of final bases. How long are your reads? Is it paired-end? There ...
written 14 months ago by Grinch10
0
votes
2
answers
1.4k
views
2
answers
Answer: A: Merge three assembled files (iterations) into one.
... This is an old question, but it might be useful for someone else with the same question. For StringTie merge, you need to merge all the samples, regardless if you have treated/untreated or healthy/cancer samples. What it does is, it makes a sort of reference GTF file with all the expressed transcrip ...
written 14 months ago by Grinch10
0
votes
6
answers
24k
views
6
answers
Comment: C: How To Sort Sam File
... sort: invalid option -- 'O' sort: invalid option -- 'T' This is the error I get if I try this command. I don't see -O and -T flags in the man pages on SamTools. From where you got this flags? ...
written 17 months ago by Grinch10
1
vote
1
answer
1.4k
views
1
answer
MeDIP-seq and hMeDIP-seq analysis
... Hi! I'm analysing MeDIP-seq and hMeDIP-seq data for the first time (I've analysed ChIP-seq and RNA-seq data sets before) and was wondering if people who have done it before can recommend pipelines they have used and/or programmes for quantitative comparison of ChIP-Seq data. My data set is made of r ...
medip-seq hmedip-seq chip-seq written 2.3 years ago by Grinch10 • updated 2.3 years ago by dally160

Latest awards to Grinch

Popular Question 8 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Popular Question 9 months ago, created a question with more than 1,000 views. For MeDIP-seq and hMeDIP-seq analysis
Supporter 9 months ago, voted at least 25 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Generating the output file name from the input file in bash script

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1558 users visited in the last hour