User: Seq225

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Seq22550
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Posts by Seq225

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Very low mapping rate of mRNA seq data
... ATpoint and Mehemt, thank you very much. I have talked with the sequencing core. They never depleted the rRNA. That could be the actual problem. Do you guys know any way to find out the rRNA mapping percentage of my data? Like I said, I do not have a genome sequence for this organism. Is there any ...
written 20 days ago by Seq22550
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Comment: C: Very low mapping rate of mRNA seq data
... Thank you. The reads are good quality (almost all of them). Not sure about any sort of contamination. Unfortunately, I do not have a ref genome. ...
written 21 days ago by Seq22550
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Very low mapping rate of mRNA seq data
... Hi, I have ~100 paired end mRNA seq data (150 Nt read size) that were sequenced by Illumina MiSeq. I have clipped the adapter by cutadapt. I am getting low mapping percentage. I used BWA, Bowtie2, and STAR. For STAR, I am getting 3-30% mapping. Bowtie2 ~40% and BWA 40-45%. I am using assembled tran ...
genome assembly rna-seq sequencing written 21 days ago by Seq22550
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Comment: C: Problem mapping mRNA seq data using STAR.
... Thanks you very much ...
written 21 days ago by Seq22550
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Comment: C: Problem mapping mRNA seq data using STAR.
... There are some 0 nt reads. I am sure about that. STAR (or any other aligner probably) had problem working on 0 nt reads. I am asking if they have resolved that issue? Or I have to delete those reads from my file. ...
written 23 days ago by Seq22550
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Problem mapping mRNA seq data using STAR.
... I am running STAR on paired end reads:** star --runThreadN 50 --genomeDir index --readFilesIn ASS_1_1.fq.gz ASS__1_2.fq.gz --outFileNamePrefix ASS.mapped.sam --readFilesCommand gzcat Sep 21 16:20:32 ..... started STAR run Sep 21 16:20:33 ..... loading genome Sep 21 16:20:39 ... ...
assembly alignment rna-seq written 23 days ago by Seq22550 • updated 22 days ago by RamRS18k
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Comment: C: Could someone explain this perl command?
... Great. Thank you! I will try these... ...
written 7 weeks ago by Seq22550
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Comment: C: Could someone explain this perl command?
... Its ok. Thanks very much Ram!! ...
written 7 weeks ago by Seq22550
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Comment: C: Could someone explain this perl command?
... Thanks very much. I will replace the print with qx. Also, if you don't mind and have time to spend, is it possible to point out the other problems? Thanks like a ocean!! ...
written 7 weeks ago by Seq22550
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Comment: C: Could someone explain this perl command?
... I am very confused here. I think the main execution here is based on the perl script. I have provided it below. The entire idea is to extract sequences with “Complete Proteome” in the Keyword from files downloaded (Swiss-Prot and TrEMBL). All I am trying to do is repeating some analyses from this ...
written 7 weeks ago by Seq22550

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Popular Question 12 months ago, created a question with more than 1,000 views. For HOMER annotatePeaks.pl problem
Popular Question 12 months ago, created a question with more than 1,000 views. For De Novo Assembly of small RNA Reads (Illumina)

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