Datasets:

cannin

/

biostars_qa

like 2

Dear all, I would like to align some reads to a reference using STAR. The following command works perfectly: STAR --genomeDir output/spiking/index/star --readFilesIn reads.fastq --outFileNamePrefix outputFolder --runThreadN 8 > message.txt However, the following command does not work: STAR --genomeDir output/spiking/index/star --readFilesIn reads.fastq.gz --outFileNamePrefix outputFolder --runThreadN 8 > message.txt Error: the read ID should start with @ or > Presumably, STAR expects a FASTQ file and not a fastq.gz file. Does anybody know how to get round this in an efficient way? Thanks. C.

add `--readFilesCommand zcat` in your commandline

biostars

{"uid": 243683, "view_count": 24741, "vote_count": 3}

<p>Do you know any <strong>public</strong> scientific SQL server ?</p> <p>for example, I would cite:</p> <ul> <li>UCSC <a href='http://genome.ucsc.edu/FAQ/FAQdownloads#download29'>http://genome.ucsc.edu/FAQ/FAQdownloads#download29</a></li> <li>ENSEMBL <a href='http://uswest.ensembl.org/info/data/mysql.html'>http://uswest.ensembl.org/info/data/mysql.html</a></li> <li>GO <a href='http://www.geneontology.org/GO.database.shtml#mirrors'>http://www.geneontology.org/GO.database.shtml#mirrors</a></li> </ul> <p>(I'll give a +1 to each correct answer)</p>

<p><a href="http://biowarehouse.ai.sri.com/PublicHouseOverview.html">PublicHouse</a> - uses the <a href="http://biowarehouse.ai.sri.com/index.html">BioWarehouse</a> system; requires user registration.</p>

biostars

{"uid": 474, "view_count": 11197, "vote_count": 22}

Hi, I want to use bedops to analyze some of the .bed files from ChIP-seq, but one of the files I can't go through the analysis, even can't sort-bed. It keeps saying the BED row length exceeds capacity at line 1. It doesn't help even after I deleted the first row of my .bed file. ``` unknownb8f6b1106ced:chip-seq fuxiaoyong$ sort-bed era_inpegf_mcf7_n3_hg18_f20_nr.bed BED row length exceeds capacity at line 1 in era_inpegf_mcf7_n3_hg18_f20_nr.bed. Check that you have unix newlines (cat -A) or increase TOKENS_MAX_LENGTH in BEDOPS.Constants.hpp and recompile BEDOPS. ``` I am very new for using tools to analyze NGS data, even for the Mac OS X system. So, please help me and your detailed explanation will be greatly appreciated!!

Hello, As discussed, the problem was owing to Excel messing up your BED file. To delete blank rows from your BED file, use the following command: sed '/^$/d' <era_inpegf_mcf7_n3_hg18_f20_nr.bed >era_inpegf_mcf7_n3_hg18_f20_nr_NoBlanks.bed Or, you could also manually remove blank lines (a tedious process) by opening the file in TextWrangler.

biostars

{"uid": 108741, "view_count": 3131, "vote_count": 1}