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Parse Error At Line Sequence And Quality Are Inconsistent

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Your symptom is often the result of piping stderr to same same stdout in a previous process. 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 Best, Xiaolong ------------------ 原始邮件 ------------------ 发件人: "Colin Hercus";; 发送时间: 2013年9月13日(星期五) 中午11:30 收件人: "崔晓龙"; 抄送: "samtools-help"; 主题: Re: [Samtools-help] 回复: Questions about SAMtools Hi Xiaolong, This line is missing the readname from Standardize and globalize service processes across IT 3. Source

You seem to have CSS turned off. So, I'm looking forward to your reply. how to use htslib to convert fastq to bam file I want to write some c code to convert fastq to unmapped bam file. Thanks in advance! Discover More

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Myron Peto myronpeto View Public Profile Send a private message to myronpeto Find More Posts by myronpeto 02-02-2012, 01:11 PM #2 swbarnes2 Senior Member Location: San Diego Join Now I encounter a question about SAMtools when I tried to convert .sam file into .bam file: > > $ samtools view -h accepted_hits.bam > zz.sam > $ samtools view -bS Continue Blackwell 2013-02-05 12:52:17 UTC PermalinkRaw Message In fact, it occurs to me to ask whether the unix "locale" under whichsamtools and bwa were compiled contains any multi-byte characters inthe collating sequence.

which tools are suitable to visualize our mapping results I'm not sure what you mean here - what do you want to see? Is there something obviously wonky about it? -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact Thread From the record in the .sam file it seems the sequence and quality strings are of different length and the problem is upstream of the conversion from .sam to .bam Regardless, 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

Error In Sam To Bam Conversion I want to convert Sam file into Bam. Hello, I have some SAM files which lack the header. Password Register FAQ Community Calendar Today's Posts Search You are currently viewing the SEQanswers forums as a guest, which limits your access. http://seqanswers.com/forums/showthread.php?t=17353 This flag is for 1.5+ and now CASAVA can get qualities upto 41 HTH dave #Edit: sorry, I meant 1.3+ and not 1.5+ Last edited by dnusol; 02-03-2012 at 03:57 AM.

Please don't fill out this field. Please don't fill out this field. Here is the stripped-down program.... #include #include "sam.h" int main(int argc, char **argv) { samfile_t *sam = samopen(argv[1], "r", NULL); if(sam == NULL) { fprintf(stderr, "file open error: '%s'\n", argv[1]); No, thanks SourceForge Browse Enterprise Blog Deals Help Create Log In or Join Solution Centers Go Parallel Resources Newsletters Cloud Storage Providers Business VoIP Providers Call Center Providers Thanks for helping

Samtools Mpileup

I have tried the following commands too - samtools view -bt Pan_troglodytes.fa.fai -S ref_aln_scaf.sam -o ref_aln_scaf.bam samtools view -bt Pan_troglodytes.fa.fai ref_aln_scaf.sam > ref_aln_scaf.bam The sam file has some words such as https://sourceforge.net/p/bio-bwa/mailman/message/27834048/ I think BAM is a binary version of SAM that allows generating an associated index, so that you (or some visualization tool) can retrieve portions of it without processing the rest. Samtools Manual Type "show warranty" for details. Please don't fill out this field.

how does the SAM file EOF marker look like? http://kiloubox.com/parse-error/parse-error-line-2.html Create a password I agree to the terms of service Signed in as (Sign out) Close Close Post comment Submitting... I understand that I can withdraw my consent at any time. Already have an account?

After looking ... Sign up for the SourceForge newsletter: I agree to receive quotes, newsletters and other information from sourceforge.net and its partners regarding IT services and products. Parse error at line *3512359*: sequence and quality are inconsistent createbam.sh: line 1: 10236 Aborted (core dumped) samtools view -bS -t virus-db.fasta.formatted.fixedlen.fa.fai S3-n4-o2-e2.sam -o S3-n4-o2-e2.bam [bam_header_read] EOF marker is absent. [bam_sort_core] have a peek here Sign up for the SourceForge newsletter: I agree to receive quotes, newsletters and other information from sourceforge.net and its partners regarding IT services and products.

My sam file after headers looks like this - scaffold1 4 * 0 0 * * 0 0 55278387 0 - 100 #DOWN 68667525:5:56 68667525 127 + 556 #DOWN 63995574:5:107 60040051:2:45 Best wishes, Xiaolong ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. You seem to have CSS turned off.

ITMAT Applications member khayer commented May 2, 2012 The errors disappeared by Including read groups: @RG\tID:foo\tSM:bar Setting the Map Quality to zero Adding the NM tag Fixing some of the bit

adds an index, so that you can retrieve portions of it without filtering the rest." what index you are talking about (is it related with reference index or some thing else) They'll go into 2.00_10. Any other ideas are most welcome. You seem to have CSS turned off.

My question is, how can I use cuffdiff when my reference genome is made up of three different seq... Please refer to our Privacy Policy or Contact Us for more details You seem to have CSS turned off. Parse warning at line 49709458: mapped sequence without CIGAR Parse error at line 49709458: sequence and quality are inconsistent Aborted The accepted_hits.bam is generated from TopHat for RNA-seq reads. Check This Out Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk_______________________________________________ Samtools-help mailing list [email protected]

Continue anyway. > > ~ > > > > Cheers > > kevin > > > > ------------------------------------------------------------------------------ > > This SF.Net email is sponsored by the Verizon Developer Community > Converting Sam Files To Bam Files - Reproduce Results Nature Paper: Transcriptome Genetics Using Second Generation Sequencing In A Caucasian Population I want to reproduce the results that people achieved in What I have done are: 1... Please don't fill out this field.

about • faq • rss Community Log In Sign Up Add New Post Question: Samtools Api: Sequence And Quality Are Inconsistent 1 3.3 years ago by Daniel Standage ♦ 3.6k Davis, Next, I*samtools view -bS file.sam > file.bam*using samtools version 0.1.18 (r982:295).I could convert 443 out of the SAMs into BAMs without any complaints, butget 5 different error messages for the remaining Similar Threads Thread Thread Starter Forum Replies Last Post NGS whole genome sequence versus sequence capture for quality control houkto Bioinformatics 0 02-02-2012 04:16 AM Anyone knows sequence quality score 0-99? That is really confusing and I have searched SEQanswers but didn't find any answers.

dnusol View Public Profile Send a private message to dnusol Find More Posts by dnusol 02-06-2012, 09:05 AM #9 myronpeto Member Location: Portland, OR Join Date: Sep 2011 Posts: