User: anc.informatics

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Posts by anc.informatics

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How to map Arabidopsis reference ids to locus id for the newer arrays
... I normalized a batch of newer Affymetrix microarray data using **oligo package**. However, unlike the Affy package that provides the probe ids, oligo gave the reference ids corresponding to gene expression (for ex, 13320001, 13320003). In this case, how can I retrieve locus id or probe ids for each ...
normalization oligo package id microarray written 19 days ago by anc.informatics0 • updated 11 days ago by Biostar ♦♦ 20
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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 10 weeks ago by anc.informatics0 • updated 10 weeks ago by jared.andrews071.8k
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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 14 months ago by anc.informatics0
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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 14 months ago by anc.informatics0
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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 14 months ago by anc.informatics0
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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 14 months ago by anc.informatics0 • updated 14 months ago by finswimmer9.9k
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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 15 months ago by anc.informatics0
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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 15 months ago by anc.informatics0 • updated 15 months ago by Martombo2.4k

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Why Warning: reads with missing mate encountered is occured in HTSeq?
Popular Question 14 months ago, created a question with more than 1,000 views. For Why Warning: reads with missing mate encountered is occured in HTSeq?

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