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Parse Error At Line Invalid Cigar Character

m_elena_bioinfo View Public Profile Send a private message to m_elena_bioinfo Find More Posts by m_elena_bioinfo 11-12-2009, 03:57 AM #2 dawe Senior Member Location: 4530'25.22"N / 915'53.00"E Join Date: Apr Briefly describe the problem (required): Upload screenshot of ad (required): Select a file, or drag & drop file here. ✔ ✘ Please provide the ad click URL, if possible: Home Browse Technical questions like the one you've just found usually get answered within 48 hours on ResearchGate. Thanx! http://kiloubox.com/parse-error/parse-error-at-line-1-invalid-cigar-character.html

What is the actual problem here? 1 vote Vote Vote Vote Vote Sign in prestine Your name Your email address Check! All Rights Reserved. Please don't fill out this field. Any suggestions? https://www.biostars.org/p/65074/

Samtools Adding Head reduces file size Hi all, I'm trying to convert my SAM to BAM files using samtools, to subsequently view them in I... Single Sign On provided by vBSSO To use Google Groups Discussions, please enable JavaScript in your browser settings, and then refresh this page. . I can only think that the problem is the header of sam file. Sign up today to join our community of over 11+ million scientific professionals.

Create the index files with samtools faidx sequence.fa This creates the index file *.fai. Reason: ver ramouz87 View Public Profile Send a private message to ramouz87 Find More Posts by ramouz87 11-19-2010, 07:10 AM #7 m_elena_bioinfo Member Location: Ospedali Riuniti di Bergamo, Similar Threads Thread Thread Starter Forum Replies Last Post sam2bam error Hit Bioinformatics 1 07-06-2011 12:50 AM Thread Tools 11-12-2009, 03:21 AM #1 m_elena_bioinfo Member Location: Ospedali Riuniti Please compare the input to the spec in: > samtools.sourceforge.net/SAM1.pdf. > > - tom blackwell - > > On Wed, 14 Sep 2011, Peter Cock wrote: > > > On Wed,

Sam To Bam I sequenced a mito genome using paired end method on the mi-seq I mapped all the reads back to re... Please take a look at my errors: http://goo.gl/Oa2IxR In the link, you will see 2 ima... Why Bam File Been Seperated By Samtools I run the following command using BWA version 0.7.5: # transform the SAM file to BAM ~/bin/samt... Understanding the source of the problem and what it is all about provides more headache to the users.

You must know that there are times where downloaded files are not functional so you have to cope with it. ADD COMMENT • link modified 3.7 years ago by Alex Reynolds ♦ 15k • written 3.7 years ago by Rohit • 620 0 3.7 years ago by SK • 100 Germany I have sam/bam files with reads mapped to human genome from a RNA-seq experiment. Click here to register now, and join the discussion Community Links Members List Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page...

Terms Privacy Opt Out Choices Advertise Get latest updates about Open Source Projects, Conferences and News. I used Tophat2 in my work. I am using command $ samtools view -b -S -o bowtie.glob.bam bowtie.glob.sam but getting error Parse error at line 25645: invalid CIGAR character Could someone please help me to solve this Create a password I agree to the terms of service Signed in as (Sign out) Close Close 1 vote 2 votes 3 votes Remove votes You have left! (?) (thinking…) Rohit

Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. this contact form So with the ... SAM-to-BAM error with custom reference Dear Galaxy Biostar team, I'm seem to be having a problem running Samtools SAM-to-BAM conversion... You seem to have CSS turned off.

Second: it seems that the result of CRAC is not reproducible and depend on the number of threads used, i found a difference in size of the output file: 526909440 Jun Parse error at line 9962791: sequence and quality are inconsistent [bam_sort_core] merging from 7 files... [samopen] SAM header is present: 25 sequences. [sam_read1] reference 'XU:i:1' is recognized as '*'. But the program doesn't run and the error this time is: [sam_header_read2] 735 sequences loaded. [sam_read1] reference 'hsa-mir-182' is recognized as '*'. have a peek here I'm trying to align the denovo assembly scaffolds I have generated to the available reference genome.

References & Information; Problem with sam to bam converison after alignment of scaffolds to … - https://hengli.uservoice.com/forums/152783-general/suggestions/5363330-problem-with-sam-to-bam-converison-after-alignment Error in Sam to Bam conversion. - ResearchGate - http://www.researchgate.net/post/Error_in_Sam_to_Bam_conversion HTSeq-Count Error on Cloudman ADD COMMENT • link modified 3.7 years ago • written 3.7 years ago by Ashutosh Pandey ♦ 10k 1 The manual was where I got the solution from... Or it is possible that the run simply didn't fully complete - double check that you have sufficient resource allocated (memory and available disk space).

But what can I do?

Having these kinds of errors doesn't mean that you should replace your computer, sometimes it just needs some troubleshooting effort from you. Pileup error: line length exceeds XXX in sequence YYY Hi,    I mapped my reads, filtered unpaired reads, converted to BAM and now I want to generate ... And the sameproblem came up with the satble last version of samtools...Can you help me ?FrancoisPS: I used BWA 0.5.8a for my mapping-------------------------------------------------------------------------------Start uncovering the many advantages of virtual appliancesand start May 20, 2011 Galaxy Development News Brief May 20, 2011 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy- central/wiki/Fea...

Feb 27, 2013 Can you help by adding an answer? about • faq • rss Community Log In Sign Up Add New Post Question: HTSeq-Count Error on Cloudman 0 18 months ago by madkisson • 30 United States madkisson • 30 RNA-seq analysis in Galaxy I am doing RNA-seq analysis for several mouse samples and I encounter problems during differentia... Check This Out The problem was indeed the input format which I was blindly assuming to be .sam from the aligner.

Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » Home Password Register FAQ Community Calendar Today's Posts Search You are currently viewing the SEQanswers forums as a guest, which limits your access. what is the CIGAR string? I al...

Jen, Galaxy team ADD COMMENT • link written 17 months ago by Jennifer Hillman Jackson ♦ 21k Please log in to add an answer. This might help. Abort! >samtools view -S aln.sam prova.bam [samopen] no @SQ lines in the header. [main_samview] random alignment retrieval only works for indexed BAM files. I've made BAM file using TopHat2...

Insufficient Virtual Memory The RAM of your PC is also one of the common areas where error occurs. Thanks Ramzi Last edited by ramouz87; 11-13-2009 at 04:20 AM. The Cufflinks docume... My AccountSearchMapsYouTubePlayNewsGmailDriveCalendarGoogle+TranslatePhotosMoreShoppingWalletFinanceDocsBooksBloggerContactsHangoutsEven more from GoogleSign inHidden fieldsSearch for groups or messages TomDownload Search Primary Menu Skip to content Sitemap Search for: Parse Error At Line 1 Invalid Cigar Character admin Knowing

Screenshot instructions: Windows Mac Red Hat Linux Ubuntu Click URL instructions: Right-click on ad, choose "Copy Link", then paste here → (This may not be possible with some types of Similar posts • Search » What does this HTseq-count error mean? If you would like to save money at the same time develop your technical skills, the following tips will be of big help. reference.fa has a separate reference.fa.fai file.

HTSeq-Count on Command Line Dear all So basically, I have a .bam file(cut_L7_1_5.bam) and i installed HTSeq-Count onto my lo... Should I replace these with something? Francois Sabot 2010-09-27 07:58:53 UTC PermalinkRaw Message HiThe problem is such as :''[sam_header_read2] 5300 sequences loaded.[sam_read1] reference 'contig_0001_chr01' is recognized as '*'.Parse error at line 1: invalid CIGAR characterSegmentation fault''It happens I am running HTseq-count on galaxy cloud on some BAM files generated from galaxy Tophat.

Please compare the input to the spec in: samtools.sourceforge.net/SAM1.pdf. - tom blackwell - On Wed, 14 Sep 2011, Peter Cock wrote: > On Wed, Sep 14, 2011 at 11:18 AM, Kenlee IGV can't view SAM file I'm trying to view SAM files I have got after alignment using IGV.  When I try to load the SAM fi... Feb 27, 2013 Nick Riddiford · Institut Curie Try using something like this: samtools view -bS output.sam > output.bam Feb 27, 2013 Mohamed Ashick · Institut de Génétique et de Biologie