User: anc.informatics
anc.informatics • 0
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Posts by anc.informatics
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... 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 ...
written 3 days ago by
anc.informatics • 0
• updated
3 days ago by
jared.andrews07 • 1.6k
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... 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.informatics • 0
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... 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.informatics • 0
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... 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.informatics • 0
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... 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 ...
written 12 months ago by
anc.informatics • 0
• updated
12 months ago by
finswimmer ♦ 7.8k
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... 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.informatics • 0
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... 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 ...
written 12 months ago by
anc.informatics • 0
• updated
12 months ago by
Martombo • 2.3k
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