User: wm

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wm370
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370
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China
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9 hours ago
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8 years, 4 months ago
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Posts by wm

<prev • 72 results • page 1 of 8 • next >
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Answer: A: Download NCBI GEO dataset
... That is a easy way using sra-explorer, as posted above. Here is another option: If you want to explore the submission on your own, here are some brief info: `GEO` saved the "processed data", and `SRA` saved the fastq files. So, you can get the fastq files from the `SRA` accession list for the ` ...
written 15 hours ago by wm370
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Answer: A: How to split a string and swap the result in bash
... How about try this command? $ cat in.txt 123520 T C missense Rv0104 Rv0104 protein_coding + 402Y>402H 123520T>C 199470 T G missense mce1A Rv0169 protein_coding + 313S>313A 199470T>G 199470 T G ...
written 1 day ago by wm370
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Comment: C: there is an error after samtools index
... (remove the `-n` option); It is because the `-n` option is **sorted by name**. -n Sort by read name Index, requires the bam file sorted by **Coordinates**. See the manual of samtools: [http://www.htslib.org/doc/samtools-index.html][1] > Index a coordinate-sorted BGZIP-compressed ...
written 2 days ago by wm370
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Comment: C: Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
... @genomax, Thanks, I did not consider the situation, PE reads trimmed separately, as you mentioned. And `repair.sh` is a good solution for two files, read names was messed up. my previous comment is for the situation, reads are not in correct pairs, or files are truncated. If it is true, trimmed se ...
written 3 days ago by wm370
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Comment: A: Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
... The two files fastq files might not a pair of PE reads, or one of the file is truncated. ### If not from a pair of PE reads you could check the first reads (eg: 10 reads) names. if they are identical in two files: $ zcat R_1.fastq.gz | head -n 40 | grep ^@ $ zcat R_2.fastq.gz | head -n 40 ...
written 3 days ago by wm370
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Comment: C: Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
... make sure the read number in `R_1.fastq.gz` and `R_2.fastq.gz` are identical. check is out in `fastqc` output, "Summary". What are the numbers? ...
written 3 days ago by wm370
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Comment: C: Interpretation of SRA files
... Thanks so much, I got it. ...
written 4 days ago by wm370
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Answer: A: Interpretation of SRA files
... Reads are compatible for aligners like BWA, bowtie2, etc (I tested), even if the `/1`, `/2` suffix not exists. You need to be caution, make sure the first part of name in read1 and read2 are identical, and in the same order. What you paste in the post does **not** like the first two headers, t ...
written 4 days ago by wm370
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Comment: C: Interpretation of SRA files
... 1. it is the updated version of illumina software. to my understand, the latest illumina output fastq file contains `two parts` in the name line, separated by a "white space", `the name` + `index information`. the name part are identical for read1 and read2. Only the first part will be used in furt ...
written 4 days ago by wm370
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Comment: C: How to extract intervals for regions that are masked?
... The "Genome" **subtract** the "masked" intervals are the "unmasked" intervals, this is what you want, right? You can get it using `bedtools complement` command: First, you need generate the `Genome` file for your genome $ cat in.fa >fa AGGTCGTTNNNNAACTGNNAGTC $ samt ...
written 5 days ago by wm370

Latest awards to wm

Scholar 4 days ago, created an answer that has been accepted. For A: Extract data from a large bed file
Scholar 17 days ago, created an answer that has been accepted. For A: Extract data from a large bed file
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Pheatmap Annotation
Popular Question 10 months ago, created a question with more than 1,000 views. For How Can Soap2Sam.Pl Be More Fast?
Great Question 2.4 years ago, created a question with more than 5,000 views. For Error When Install Samtools, Version `Zlib_1.2.3.3` Not Found
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Pheatmap Annotation
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Pheatmap Annotation
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Pheatmap Annotation
Supporter 4.8 years ago, voted at least 25 times.
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Error When Install Samtools, Version `Zlib_1.2.3.3` Not Found

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