User: anc.informatics

Reputation:
0
Status:
New User
Last seen:
2 days, 3 hours ago
Joined:
1 year, 1 month ago
Email:
a**************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by anc.informatics

<prev • 7 results • page 1 of 1 • next >
1
vote
1
answer
83
views
1
answer
What is the reason for big difference in DEGs estimation compared to previous estimation?
... I tried to estimate the DEGs for a set of transcriptome from the [study][1]. In the analysis pipeline, after adapter removal using Trim galore, I first mapped the reads to reference using Hisat2. Then estimated the counts using featureCounts. These raw counts were input to DESEq2 for DEGs estimation ...
tophat degs rna-seq written 3 days ago by anc.informatics0 • updated 3 days ago by jared.andrews071.6k
0
votes
0
answers
730
views
0
answers
Comment: C: Question: Error HISAT2 output for HTseq-count
... Not an answer to your question, but consider [featureCounts][1] which is an ultra fast read count program and work well with Hisat2 output SAM file. Also, it rearrange read itself and final table of read count matrix for all paired end SAM can be obtained. For ex, featureCounts -p -t exon -g ge ...
written 12 months ago by anc.informatics0
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Why Warning: reads with missing mate encountered is occured in HTSeq?
... Yes, I came to know that -T option after checking the manual. Actually I was referring to an old one. Thanks again for your help!! ...
written 12 months ago by anc.informatics0
0
votes
1
answer
980
views
1
answers
Comment: C: How to specify the sort based on name in samtools sort?
... It was a doubt from my [previous post][1]. I think i need to use -r option in HTSeq since I will sort bam file using position and not by name. [1]: https://www.biostars.org/p/285514/#285673 ...
written 12 months ago by anc.informatics0
2
votes
1
answer
980
views
1
answer
How to specify the sort based on name in samtools sort?
... I would like to know how to issue the command when sorting a BAM file based on name. The problem is that when I used the command, samtools sort -n -o WT.bam /home/exp/accepted_hits.bam It run without any error. However, when tried to index the BAM file like, samtools index WT.bam I go th ...
htseq bam samtools rna-seq sort written 12 months ago by anc.informatics0 • updated 12 months ago by finswimmer7.8k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Why Warning: reads with missing mate encountered is occured in HTSeq?
... Thanks for the explanation. May I know how the -n -o can be used in sorting? First I used -no after seeing a thread from SEQanswer but, it didn't seems sort correctly as I get error Unsorted positions on sequence #6: 5325030 followed by 5325016 samtools index: failed to create index for ...
written 12 months ago by anc.informatics0
4
votes
1
answer
1.3k
views
1
answer
Why Warning: reads with missing mate encountered is occured in HTSeq?
... I was following [DESeq2 manual][1] to process my simple RNASeq paired end data that involves wil type and stress treated plant. I ran feature count using HTSeq (version 0.9.1) with the command, htseq-count -a 10 -s 'no' WT-CON.sam /home/exp/DESEQ2/genes.gtf > WT-DESeq.txt I noticed a **Wa ...
htseq alignment sam rna-seq written 12 months ago by anc.informatics0 • updated 12 months ago by Martombo2.3k

Latest awards to anc.informatics

Popular Question 12 months ago, created a question with more than 1,000 views. For Why Warning: reads with missing mate encountered is occured in HTSeq?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1644 users visited in the last hour